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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattatgaaaatttaatatccattgttaatgaatcaattatgacaatacgtatatatgataattttgtaatgcttttaatttcttttatttttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACATGGCCCTTGAAAGGTTGCTGT

Basic information

species Glycine max
transcript GLYMA06G17470.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G17470.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g00610.t01 (Vitis vinifera), 3'ss of exon 4
----------------------aattatgaaaatttaatatccattgttaatgaatcaattatgacaatacgtatatatgataattttgtaatgcttttaatttcttttatttttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACATGGCCCTTGAAAGGTTGCTGT-
                      |||||   || | |  |||  |   || ||  | |  |  | || ||    || | |   ||  |     | | || | || || ||   |||| |||||||||| ||||| || |||||||| || || ||||||  ||||||||| |   ||| |||| ||||||||||||||||| |||| ||||||| | | |||  
gtattatcatcttggcttaaaaaattactgaa-tatggtata-aacattcatcgacctctcttcactattgtaattttttgaaaagtaaatgttcattaagttactgttggatttg-tacagGTACAAAAACTTGTGGAGATGGGCTTCCCTGAAGCTTCAGTAAGGAGTACCCTGGCAGCTTTTGGTGGTGATGAAAACTTGGCTCTTGAAAAGCT-CTGCT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|8402902|gb|BE058536.1|BE058536
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|17152827|gb|BM142760.1|BM142760
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|4397642|gb|AI496639.1|AI496639
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAA
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAA
EST: gi|151403796|gb|EV273606.1|EV273606
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|7028702|gb|AW458485.1|AW458485
EST:     ACTGGACAGAGAGTTGTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAC                         GTACGAGAA-CTCGGTGAGATG
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTAC-AGAAACTCGTTGAGATG
EST: gi|8402482|gb|BE058116.1|BE058116
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|15813074|gb|BI785349.1|BI785349
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|298189987|gb|HO032108.1|HO032108
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAG
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAG
EST: gi|193566075|gb|FK525936.1|FK525936
EST:     TTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: TTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|254313570|gb|GR831199.1|GR831199
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|192304311|gb|FG993567.1|FG993567
EST:     GGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCA-T
genomic: GGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
EST: gi|58022999|gb|CX709740.1|CX709740
EST:     ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAG                         GTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT
genomic: ACTGGACAGAAAGTTTTGCCAAGGCTTCGTCTCGTGGGATTGAAGATAAGgtactaagct ... tttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacgtatatatgataattttgtaatgcttttaatttcttttatttttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACATGGCCCTTGAAAGGTTGCTGT
                            ttttaat  putative branch site (score: 3)
                           cttttaatttctttta  CT-rich tract
     tatatatgataatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattatgaaaatttaatatccattgttaatgaatcaattatgacaatacgtatatatgataattttgtaatgcttttaatttcttttatttttggtacagGTACAGAAACTCGTTGAGATGGGATTTCCAGAAGCTCGAGTAAGGAGCATTTTGGAAGCTGTTGGTGGTGATGAAAACATGGCCCTTGAAAGGTTGCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG