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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcatcatacaacttactcttaattcattactataagtcagaagaaaattattatcctaaaattgtttatttcttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGGTTCGGCCACAACAATCGGCTTGGTTGTTCATCTGTGTCACAAGGAAGCA

Basic information

species Glycine max
transcript GLYMA10G30440.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30440.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0081g00010.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gttagtcatcatacaacttactcttaa----ttcattactataagtcagaagaaaattattatcctaaaattgtttatttcttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGAT---TTTAGGGTTCGGCCACAACAATCGGCTTGGTTGTTCATCTGTGTCACAAGGAAGCA
                         |  | |||||     |||   | ||    ||||  ||| |    | ||   ||  | || |  |    |  || ||   |      |||| |||||||| ||||| |||||||||||||||||||  ||  |    |  |  ||  | |||  | |         |  |  || ||| |   || ||| |  
gttagtcatatatacttgctgcaactcatgatcattatggttatgttcaaaattttcaccacttttg--ctgacttaatctcttgtatttgcttgattaatcaatggcatgcagCCCCAAGAGCAGTGGAGAAGTGCAAGAACAGAAGCTAGAGGCACCCATCCACAGTCTGCCCATCAAAGGAAAGCCAGAAG--CAGCTGAGGATCATGGATGG-
















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|207831482|gb|GD803412.1|GD803412
EST:     ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTG                         CACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
genomic: ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTGgttagtcatc ... ttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
EST: gi|5606447|gb|AI900481.1|AI900481
EST:     ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTG                         CACCAAGAGCCGTGG
genomic: ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTGgttagtcatc ... ttattcacagCACCAAGAGCCGTGG
EST: gi|12689680|gb|BG156016.1|BG156016
EST:     ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTG                         CACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
genomic: ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTGgttagtcatc ... ttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
EST: gi|31309253|gb|CD394456.1|CD394456
EST:     ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTG                         CACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
genomic: ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTGgttagtcatc ... ttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
EST: gi|10708992|gb|BF008777.1|BF008777
EST:     ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTG                         CACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGC
genomic: ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTGgttagtcatc ... ttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGC
EST: gi|8402213|gb|BE057847.1|BE057847
EST:     ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTG                         CACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG
genomic: ATCATGCCAGCGCCTTCGCATAATGAAAGGTTCTGAGGCTATCGGCCTTGgttagtcatc ... ttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactataagtcagaagaaaattattatcctaaaattgtttatttcttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGGTTCGGCCACAACAATCGGCTTGGTTGTTCATCTGTGTCACAAGGAAGCA
                          tcctaaa  putative branch site (score: 2)
                                     tttatttcttattc  putative PPT
             aagaaaattattatcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcatcatacaacttactcttaattcattactataagtcagaagaaaattattatcctaaaattgtttatttcttattcacagCACCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGTGATTTTAGGGTTCGGCCACAACAATCGGCTTGGTTGTTCATCTGTGTCACAAGGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA