Sequence
atgc intronic sequence ATGC exonic sequencegtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctattctgtaagtttaattttcatatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
Basic information
species | Glycine max |
transcript | GLYMA08G09050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 4
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttg-tgtgttggtcaagattttcatgtgtgaatctattctgta---agtttaattttcatatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
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--------------------------------------------------gtaacactgccttttggtaaatgtggccagacttatctatttggtactgtaatgtatacagacttataaccataccttcttggtgtaatgc-caatagGGATATCATTCGTGGGAGTCCAGATGTCAAATGGGAAAGCATTAAAGGTTTGGAGAATGCAAAGCGTCTTCTGAAAGAAGCAGTTGTGATGCCTATAAAA
upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 4
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctattctgtaagtttaattttca--tatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
|| ||| | | ||| ||| | | | || ||| | ||||| || | | || | | ||||| || ||||| || |||||||||||||| |||||||||||||| || | |||||||||||||| | || |||||||| ||||| ||||| || |||
----------------------------------------------------------gtaattcaagattca--caaactttcgaaaaatagg---aaagcacaaatttggccattgactatatattcttgccttcatctttcagGGACATTATTCGCGGCAGTCCAGATGTGAAATGGGAAAGCATCAAAGGACTGGAGAATGCCAAACGCCTTCTAAAAGAGGCAGTTGTCATGCCCATAAAG
upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 3
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctattctgtaagtttaattttcatatatgtttgtcattgcacatct-tagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
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-----------------------------------------gtaaactgtttcaaaa---tctgtacatgaca-tcaatagtgcggtactgtaatgtattctcga---ctgctgttactatagcttccttctccaatgcctacagGGATATAATTCGTGGAAGTCCAGATGTTAAATGGGAAAGCATAAAAGGTCTGGAGAATGCAAAGCGTCTTCTCAAAGAAGCAGTTGTAATGCCAATTAAA
upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G022777_T01 (Zea mays), 3'ss of exon 4
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctattctgtaagtttaattttcatatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
| | | | | ||| | |||| | | | | ||| ||| || | ||| ||||| | | | |||||||| ||||| || || ||||||||||| ||||| |||||||| || | || ||||| ||||| | || |||||||||||||| ||||| || |||
-----------------------------------------------------gtaatctaaacatcattgtggctttaacattcagggacgg-tgtggtctagctgttgaaacattttat---cccatcatttggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACTGGAAAATGCAAAACGCCTTCTAAAAGAGGCTGTTGTCATGCCCATAAAG
upper sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 4
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctat--tctgtaagtttaattttcatatatgtttg--tcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
|||| | || | | |||| | ||| | ||| | | | || | || ||| || || ||||||||| | || | |||| || || || ||| | | | | ||||| || ||||||||||||||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||| | || ||||| || ||||| ||||| || |||
gtaattgaacttcttacttt----ggacctgtaatatatctgttatttttgca-atctgtattgtgcatgt-ggccaggattttcatattctaacagaagatctgaaaattgtatac-catgcttcctcgcgttattgcctgtcc-agGGATATCATTCGTGGGAGTCCAGATGTGAAGTGGGACAGCATCAAGGGTTTAGAGAATGCCAAACGTCTGCTTAAAGAAGCAGTTGTCATGCCAATAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatctattctgtaagtttaattttcatatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
gtttaat putative branch site (score: 4)
tattctgtaagtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattttctctcaatctcttcaacacctctgatagaactgatgactacatggagaagttatttgtgtgttggtcaagattttcatgtgtgaatctattctgtaagtttaattttcatatatgtttgtcattgcacatcttagGGATATCATTCGTGGAAGTCCAGATGTGAAGTGGGAAAGCATCAAGGGGTTAGAGAATGCCAAACGTTTACTGAAAGAGGCTGTTGTGATGCCGATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT