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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcctgttataaaccattgtttttcttttaaaattttcatttttattgtagtctatcttgtgttgcacacatgtttctgtgattaattctgcatgcctgattgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGATATCAAGGACTCTACTGGTATAGAGGGCAAGGAATTGAGAAGGACTCTGC

Basic information

species Glycine max
transcript GLYMA15G10030.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10030.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 12
gttggcctgttataaaccattgttt-ttcttttaaaattttcatttttattgtagtctatcttgtgttgcacaca-tgtttctgtgattaattctgcatgcct---gattgtg-ctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGATATCAAGGACTCTACTGGTATAGAGGGCAAGGAATTGAGAAGGACTCTGC
||||| || || || ||  |||||| |||||||    |     |||||  ||   | |||       ||  |||| || ||  ||| | || | |       |   |  |||| || |||||||||||  | ||| | || ||||||||  | || || |||||||||||||| |||||||||||||| || ||||  ||||| ||||||||||||||||
gttggtcttttctagacacttgtttattctttttctttccatgtttttcctgagttttattaatccctgtgcacaatgctttagtgctcaagttttagcattttgggggtgtgtctgcagACTGTTGTCTTGATGCTGTTTAATGATGCGCAAAAGCTTAGCTTTCAAGATATTAAGGACTCTACTGGCATTGAGGATAAGGAGTTGAGAAGGACTCTGC
















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|19934696|gb|BQ079726.1|BQ079726
EST:     AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAG                         ACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
genomic: AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgt ... tgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
EST: gi|17400275|gb|BM177057.1|BM177057
EST:     AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAG                         ACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
genomic: AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgt ... tgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
EST: gi|193639977|gb|FK590138.1|FK590138
EST:     AGGCAGAGTTTCCT-AAGGG-AAAAGGAGTTGGCTGTCTCCCTATTTCAG                         ACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
genomic: AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgt ... tgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
EST: gi|7028742|gb|AW458525.1|AW458525
EST:     AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAG                         ACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
genomic: AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgt ... tgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
EST: gi|151395410|gb|EV265287.1|EV265287
EST:     AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAG                         ACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
genomic: AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgt ... tgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
EST: gi|151404598|gb|EV274412.1|EV274412
EST:     AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAG                         ACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT
genomic: AGGCAGAGTTTCCTAAAGGGAAAAAGGAGTTGGCTGTCTCCCTATTTCAGgttggcctgt ... tgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtgttgcacacatgtttctgtgattaattctgcatgcctgattgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGATATCAAGGACTCTACTGGTATAGAGGGCAAGGAATTGAGAAGGACTCTGC
                       tgattaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggcctgttataaaccattgtttttcttttaaaattttcatttttattgtagtctatcttgtgttgcacacatgtttctgtgattaattctgcatgcctgattgtgctccagACTGTTGTTCTTATGTTATTCAATGATGCTGAGAAACTAAGCTTTCAAGATATCAAGGACTCTACTGGTATAGAGGGCAAGGAATTGAGAAGGACTCTGC

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