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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA

Basic information

species Glycine max
transcript GLYMA13G06920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g41300.1 (Oryza sativa), 3'ss of exon 2
--ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcatgttttgtgttt-ttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
| |||| | | || | | || | || | | || | |||| |||| | | | ||| |||| | | | ||||||||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||| |||||||||||||||||||| |||||||||||||| |
atgttattgctttcattagtgggc-atggcatcctcgtttgtaactatggctatttggcatatttgctg--agactaacttcaacttgttcatacttgtccagCCAAGCTGGCGCAGGCCCAAGGGTATTGACTCCCGTGTCAGGAGAAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGTTACGGCTCAGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g32500.1 (Oryza sativa), 3'ss of exon 2
-ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaag-taatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
| || | | || | | | | | | | | | | ||| |||| | | | | | | || | |||| | || | || ||||||||||||| || ||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| || |||||||| |
ttttatatcgttttcagtctgcatcctagtcac--gccatgtattgtcagtttttgtttgtgtggacacaagggctcattttcatttgcactgtttctgtagACAAGCTGGCGCAGGCCAAAGGGTATTGACTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACCTTGATGCCCAACATTGGATATGGTTCTGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g32520.1 (Oryza sativa), 3'ss of exon 2
-----ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
|| || | ||| | | ||| | | ||| || || ||| | | || || || | | | | ||| | | || |||||||||||||||| ||||||||||| || ||||||||||| |||||||| |||||||| ||||||||||| ||||| ||||| || |||||||| |
ggatcatattttggtgttttttgttcttaatatgtttc-gtgctatgtttgccgaagcag--caatctgatttgtaatggtttacttctaccgtta--cgtgtagACAAGCTGGCGCAGACCAAAGGGTATTGACTCACGTGTCAGGAGGAAGTTCAAGGGATGCACATTGATGCCCAATATTGGATATGGTTCGGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os09g32532.2 (Oryza sativa), 3'ss of exon 1
ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcatgttttgtgtttttct---tacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
|||| | | || |||||| || | | | |||| | || | |||| | | ||| | || || | || ||||||||||||| || |||||||| || || |||||||||||||||||||| ||||||||||||||||| || ||||| ||||| || |||||||| |
---tgctgatgatttgtttctaacttgaatacacttctccgcttatttcttttgtgtgctgccttgcttaaatttggtgttctttttacttccctatatgtagACAAGCTGGCGCAGGCCAAAGGGTATCGACTCCCGTGTCAGGAGAAAGTTCAAGGGATGCACTTTGATGCCTAATATTGGCTATGGTTCTGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G155931_T03 (Zea mays), 3'ss of exon 1
-ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatt-tgaaattggttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
| | | || || || | || | | | | || || | | | | |||||| || | | | ||| || || ||||||||||||||||||| || ||||||||||| || ||||||||||| |||||||| |||||||| ||||||||||||||||||||||| || |||||| |
tgcagacatctattgagcttgtttttcttataccatttctttgtatttatttccctccatagagtaattctaa-gttctgacttgttg-attctttgtacagCCAAGCTGGCGCAGGCCAAAGGGTATTGACTCCCGTGTCAGGAGGAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGTTATGGTTCTGACAAGTCGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: AC197246.3_FGT003 (Zea mays), 3'ss of exon 1
ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttg-gttctaaag---taatcatg-ttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
||||||| || | | || | | | || | || | ||||| || ||| ||| | | | || || ||||||||||||||||||| || ||||||||||| || ||||||||||| |||||||| |||||||| |||||||||||||||||||| ||||| ||||| ||
-----tggatgtttaacccatatctttgtgtttatctccctctatatcattatctataattctatattctagaggactaactatgactgtttattgtttgtacagCCAAGCTGGCGCAGGCCAAAGGGTATTGACTCCCGTGTCAGGAGGAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGTTACGGCTCTGACAAATCAA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G115901_T01 (Zea mays), 3'ss of exon 2
ctaattggatgtgtaggtt----acttgttgaatgcaagtgttaa-gtgatttgaaattgg---ttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
|||| | || | | |||| | | | || | || || | || | | || || ||| |||| | | ||| | ||||||||||||||||| ||||||||||| || || ||||||||| | |||||||| |||||||| |||||||| |||||||| |||||||| |||||||| |
--------gtgtgcaactttctaattcgttgggtccctatatttatgtcatctagcataaacattcctattaattttaagctaattttaccaatgctgttttctgcagCCAAGCTGGCGCAGGCCCAAGGGTATCGACTCCCGTGTCAGGCGGAAGTTCAAGGGATGCACCTTGATGCCTAACATTGGATATGGCTCTGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G065868_T04 (Zea mays), 3'ss of exon 2
ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattg-gttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
| || | | | | | | || | | || ||| || || | | | || | | | ||| ||||| || | | ||| | |||||||||||||||| ||||||||||| || || || |||||| | |||||||| |||||||| ||||||||||||||||| |||||||| |||||||| |
atgggcacatctttccaatgcattggcactgtatat-ttgagtcatctgcactagcatttctgtctgttgaaactaatcttgctgacaatgttttctgtagCCAAGCTGGCGCAGGCCCAAGGGTATCGACTCCCGCGTCAGGCGTAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGATATGGCTCCGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G047971_T01 (Zea mays), 3'ss of exon 2
ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttcta--aagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
| | ||| | | ||| || | | ||| || || || | | | |||| || | ||| | ||||||||||||| || ||||||||||| || || || |||||| | |||||||| |||||||| ||||||||||||||||| || ||||| |||||||| |
-gtagtagatatcctataaaaggattgg-cacagctatccagttcaactgcataaacatttctgctcgttgcagctaattttgccgataatgttttgtgtagCCAAGCTGGCGTAGGCCCAAGGGTATCGACTCCCGCGTCAGGCGGAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGATACGGCTCTGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0260g00080.t01 (Vitis vinifera), 3'ss of exon 1
ctaattggatgtgtaggtt--acttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcatgttt-tgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
| |||| |||| | |||||||| | | |||| || |||||| | | | ||| | |||| | | | ||| | | |||| | | |||||| || |||||||||||||||||||| || ||||| |||||||| ||||| | | |||||||||||||||||||| ||||||||||| |
tttgttgg-tgtgctatcttggcttgttga-tattccttttaaatggagaacaattggat-tgctagtttgctactaatagaatgtgtacttttctgtgacagTCTAACTGGCGAAGGCCCAAGGGTATTGATTCTCGGGTGAGGAGGAAGTTCAAGGGATGTGTTCTCATGCCCAACATTGGTTATGGTTCAGACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S505_19V6.1 (Physcomitrella patens), 3'ss of exon 1
ctaattggatgtgtaggttacttgttgaatgcaagtgt-taagtgatttgaaattggttgttttggttctaaagtaatcat--gttttgtgtt-tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
||| ||| | ||| ||||| | || | | || | ||| || || | | | | | || || ||| || ||| ||| |||| | || || ||||||||||| ||| | || | | ||||| || || ||||||||||||||||| ||||| |||||| ||||||| |
----ttgatgttgtggtttagggtttgaacgtgcctgcactacttgttgtttgtgaaatgtcacatctcatgagagaactttgggtgagtattgtttgtttcagACAAACTGGAGGAGGCCTAAGGGTATTGACTCTAGGGTTCGCCGCAAGTTTAAGGGCACTACTTTGATGCCCAACATCGGTTACGGCTCAAACAAGAAGA

upper sequence: GLYMA13G06920.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S98_19V6.1 (Physcomitrella patens), 3'ss of exon 1
ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcat-----gttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
|| || | |||| || || | | | ||| |||||| |||| | | || | | | | | | ||| | | ||| ||| | | ||| | || || |||||||| |||||| | || | | ||||||||||| ||||||||||||||||||||||| |||||| ||||||| |
---tgcggctgatttggtt-ctgaacgagccctcagaattgatttttttaaattg-ttgtacggctgctgacgagagttttggccggtgtgtatgtctctgtcagACGAATTGGAGGAGGCCAAAGGGTATCGATTCTAGAGTTCGTCGTAAGTTCAAAGGCACTACTTTGATGCCCAACATTGGTTACGGCTCAAACAAGAAGA

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|209702715|gb|BW652758.1|BW652758
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|192318631|gb|FK008291.1|FK008291
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|58016352|gb|CX703094.1|CX703094
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|151408512|gb|EV278320.1|EV278320
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCGGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|31459271|gb|CD401299.1|CD401299
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATTTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|192318588|gb|FK008290.1|FK008290
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|151402076|gb|EV271889.1|EV271889
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|192300686|gb|FG989658.1|FG989658
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|192300439|gb|FG987896.1|FG987896
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|192329801|gb|FK023333.1|FK023333
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|209697299|gb|BW655496.1|BW655496
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|192300759|gb|FG991126.1|FG991126
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
EST: gi|209709923|gb|BW668304.1|BW668304
EST:     GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAG                         CCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC
genomic: GCGTCAAGAAGTTTATACGCCCCCAGAGTGATCGCAAGATCTCCGTCAAGgttagttagt ... tttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaaattggttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA
                    ttctaaa  putative branch site (score: 2)
 ttttgtgtttttctt  putative PPT
 taaagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaattggatgtgtaggttacttgttgaatgcaagtgttaagtgatttgaaattggttgttttggttctaaagtaatcatgttttgtgtttttcttacagCCAAGCTGGCGCAGACCCAAGGGTATTGATTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACTTTGATGCCCAACATTGGTTATGGCTCAGACAAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - ggatgtg
- - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtt