The Gene Index Project

**The DFCI Arabidopsis thaliana Gene Index (AtGI)**

AtGI TC Report:

EST IDs are linked to AtGI EST reports. ET# s are linked to qcGene reports. GB#s are linked to GenBank accessions.

>TC284900 TC143678 TC160731 TC186478
GAAGCAAAGTAAAACCTAAAAAAAAAAAAAGACCGTAAGTAGTTACAAGGGTGGAAGTATAAAGGAGCAGTCTTTTCTTC
TTCTTTCAACCCCACGGCGCAGATCCTACGAGTTTGGTCTTTGTCTCTATCTTTTCAATCTTTCTCTCTCAATCGCTCTT
CAATTTGATAACAGCAAAGTCATGGCAGGAATGGCATCTGATGGAACTCAATATGATCCTCGTCAGTTTGATACTAAGAT
GAATGCCATTCTCGGCGAGGAAGGAGAGGAAACATTCTACACTAACTATGACGAAGTTTGCGACAGCTTTGATGCAATGG
AATTGCAACCAGATCTTCTCAGGGGTATTTATGCTTACGGTTTCGAGAAGCCTTCTGCTATTCAGCAAAGAGGAATTATT
CCATTCTGCAAGGGTCTTGATGTGATCCAGCAAGCTCAATCTGGAACTGGAAAGACCGCTACCTTTTGCTCTGGTGTTTT
ACAGCAGCTCGATATTAGTTTGGTTCAATGCCAAGCTCTTGTTTTGGCACCTACCCGAGAACTTGCCCAGCAAATTGAAA
AGGTTATGAGGGCACTTGGTGACTACCTTGGCGTCAAGGCTCAGGCTTGTGTTGGTGGAACAAGTGTTCGTGAGGATCAA
CGTGTTCTTCAGTCTGGTGTTCATGTTGTTGTTGGAACCCCTGGTCGTGTCTTTGACTTGTTACGCAGACAATCCCTCCG
TGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGATATACGACA
TCTTCCAGCTTCTTCCTTCCAAGGTTCAGGTTGGTGTTTTCTCTGCTACAATGCCTCCCGAAGCCCTTGAGATCACAAGG
AAGTTCATGAACAAACCAGTCAGGATTCTGGTCAAGCGAGACGAGCTGACTCTTGAAGGTATCAAGCAGTTTTATGTCAA
TGTAGACAAGGAAGAGTGGAAACTCGAGACACTATGCGATCTCTACGAGACACTGGCCATCACTCAAAGCGTCATCTTTG
TGAACACAAGGCGTAAGGTTGATTGGCTAACCGACAAAATGAGAAGCCGTGACCACACTGTTTCAGCTACACACGGAGAC
ATGGACCAGAACACAAGAGACATCATCATGCGCGAATTCCGCTCTGGGTCTTCCCGTGTCCTCATAACCACTGACCTCCT
TGCTCGTGGTATCGATGTTCAGCAAGTCTCTCTGGTCATAAACTTTGACCTCCCAACCCAACCGGAGAATTACCTTCATC
GTATTGGAAGAAGTGGAAGGTTTGGGAGAAAGGGAGTAGCAATCAATTTCATGACATCGGAGGATGAGAGAATGATGGCT
GATATTCAGAGGTTTTACAATGTGGTCGTTGAGGAGTTGCCAAGCAATGTTGCTGATCTTCTCTGAAGCCTTTCTTTTTT
CTGTTTTTTACTGAGAAAGTGCTGTGTTTACCCCTTTTTTTGGCAGCTTCTCTATGCTTTGATTTTTGTTTTCAGGCTAC
TACTTAGATTTATAGTTCTTGGCTAAAAGCGAACATAACTCATTACATGATTTTGCTTTTTTGGCAATCAAGAATTTCGG
CATTATTTATCTTTTTGTGAACGTGGCTTACAAGGAAGGATACTCTATGAGACTAAAGACTTTTCTCT

1=============================Open Reading Frames===========================1668

                                                                                  +1
          ===========================================================             +2
             ========          ===========                                        +3
                        =========                   ========                      -3
                                                                                  -2
                                                  ========                        -1
          ===========================================================             ESTScan(+)
                                                                                  
   ==================================================================             framefinder(+)
________________________________________________________________________________

1===================================TC284900================================1668
            1a            >                  <            19             
.......................................................<        1b        
                                    2                                    >
               3           >                                   20          >
             4          >                                  <       21        
                                       5                                    >
             6a         >
    ........................................               6b               >
                7            >
                                       8                                    >
               9            >
                  10             >
                  11             >
             12        >
            13        >
               14          >
                                         15                                    >
                                     16                            >
                                     17                            >
            18    >

                                                                                                                                                             
 #  Src  EST Id              GB#           Clone/Protein   left  right Library/Protein name
                                                                                                                                                             
 1a I024 AV831205            AV831205      RAFL09-86-K16       1   573 RAFL9
 1b I024 AV815433            AV815433      RAFL09-86-K16    1140  1552 RAFL9
 2  ETG  NP411183            AY060592      AAL31217            2  1552 At1g72730/F28P22_8 [Arabidopsis thaliana]
 3  I034 137720              DR230926      105722             88   593 CERES-148
 4  I034 137662              DR230934      105662             88   513 CERES-148
 5  I023 Ceres:42530                       Ceres:42530        89  1601 full-length cDNA from Ceres, Inc.
 6a I034 34530               DR230927      42530              89   530 CERES-130
 6b I034 993239              DR377684      42530             915  1601 CERES-130
 7  I034 137669              DR230933      105669             89   616 CERES-148
 8  ETG  NP506403            AY088176      AAM65719           89  1601 putative Eukaryotic initiation factor 4A [Arabidopsis thaliana]
 9  I034 1103141             DR230928      248507             91   614 CERES-148
10  I034 11068733            DR230929      1348318            94   708 CERES-AN65
11  I034 11061338            DR230931      1340923            94   708 CERES-AN65
12  I024 BP856924            BP856924      RAFL25-31-M06      99   500 RAFL21
13  I024 BP866902            BP866902      RAFL21-79-E05      99   480 RAFL21
14  I034 145318              DR230930      113568            107   578 CERES-148
15  ETG  NP029939            AJ010472      CAA09211          109  1668 RNA helicase
16  ETG  NP305539            AC010926      AAG51861          182  1426 putative Eukaryotic initiation factor 4A; 30924-32477
17  ETG  NP525198            AY142066      AAM98330          182  1426 At1g72730/F28P22_8 [Arabidopsis thaliana]
18  I008 8754                T45491        133A3T7           182   394 Lambda-PRL2
19  I006 AV543846            AV543846      RZ25g09F          932  1525 Arabidopsis thaliana roots Columbia
20  I02D 216d17.p1           CK118700      MPMGp2011D1721   1110  1577 AtM1
21  I024 BP587900            BP587900      RAFL15-44-F08    1238  1608 RAFL15



Sequence source codes:

I008 Michigan State University, Dept. of Biochemistry & Molecular Biology
I006 Kazusa DNA Research Institute, The First Laboratory for Plant Gene Research
I034 Ceres  Inc, 
I02D Max Planck lnstitute for Molecular Genetics, Plant Protein Chip Group, Department Lehrach
I023 Inc., Ceres
I024 RIKEN Genomic Sciences Center, Plant Functional Genomics Research Group
ETGB Expressed Transcripts from GenBank

TC sequence strand: coding strand

		Evidence for coding strand		Evidence for reverse complement		Inconclusive evidence
ESTs	5' ESTs	(used as +)	11	(used as -)	-	(5'/3' source not known)
	3' ESTs	(used as -)	3	(used as +)	1	(5'/3' source not known)
	total	14		1		3
Expressed transcripts		4		-
Predicted genes		1		-
Protein hits		5		-
Trimmed polyA/T		-		-

Tentative Annotation:
UP|Q9ZS01_ARATH (Q9ZS01) RNA helicase (Fragment), complete 0

GO annotation

GO id	GO term	EC#	Type	GOpep link	%sim	%cov
GO:0005524	ATP binding	-	M	FB\|FBgn0001942	84	93
GO:0000339	RNA cap binding	-	M	FB\|FBgn0001942	84	93
GO:0008026	ATP-dependent helicase activity	-	M	TAIR\|gene:3434200	78	79
GO:0003743	translation initiation factor activity	-	M	GeneDB_Pfalciparum\|PFD1070w	81	61
GO:0003729	mRNA binding	-	M	GeneDB_Pfalciparum\|PF14_0655	85	78
GO:0003724	RNA helicase activity	-	M	FB\|FBgn0001942	84	93
GO:0004004	ATP-dependent RNA helicase activity	-	M	GeneDB_Pfalciparum\|PFD1070w	81	61
GO:0017116	single-stranded DNA-dependent ATP-dependent DNA helicase activity	-	M	FB\|FBgn0001942	84	93
GO:0008372	cellular component unknown	-	C	TAIR\|gene:3434200	78	79
GO:0005829	cytosol	-	C	FB\|FBgn0001942	84	93
GO:0005634	nucleus	-	C	FB\|FBgn0001942	84	93
GO:0009505	cell wall (sensu Magnoliophyta)	-	C	TAIR\|gene:2030284	100	100
GO:0016281	eukaryotic translation initiation factor 4F complex	-	C	GeneDB_Pfalciparum\|PFD1070w	81	61
GO:0000381	regulation of alternative nuclear mRNA splicing, via spliceosome	-	B	FB\|FBgn0001942	84	93
GO:0006268	DNA unwinding during replication	-	B	FB\|FBgn0001942	84	93
GO:0000004	biological process unknown	-	B	TAIR\|gene:2030284	100	100
GO:0006441	binding to mRNA cap	-	B	GeneDB_Pfalciparum\|PF14_0655	85	78
GO:0007446	imaginal disc growth	-	B	FB\|FBgn0001942	84	93
GO:0006413	translational initiation	-	B	FB\|FBgn0001942	84	93
GO:0006446	regulation of translational initiation	-	B	GeneDB_Pfalciparum\|PFD1070w	81	61
GO:0002168	larval development (sensu Insecta)	-	B	FB\|FBgn0001942	84	93