Sequence
atgc intronic sequence ATGC exonic sequence...tgttaaaatatacctcatctattctatgtgtgtaattataagtcacatatatgagaatctctagtatagttatttctcactttgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
Basic information
species | Glycine max |
transcript | GLYMA15G12950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 5
tgttaaaatatacctcatctattctatgtgtgtaattataagtcacatatatga-gaatctctagtatagttatttctcactttgct--ttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
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-ctttgagttcatgtcatgtataagatgtct-taaatatgtgatctttgcgtaacggatccatccca-attcattcgttgttttgtgaactaatgtaatacagCCTACTCTATGGAGCAGAAGATTCCTCGATTGCTGGAATGGTATTGGATAGTGCTTTCACTAACTTATATGGCTTGATGATGGAGCTTGTGGATGTCTAC
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
tgttaaaatatacctcatctattctatgtgtgtaat-tataagtcacatatatgag--aatctctagtatagttatttctcactt-tgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
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--tagaagtacccct-gtccataaaatattttaaatatttaggttctatttatgtattgaattttggta-agttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 5
---tgttaaaatatacctcatct--attctatgtgtgtaattataagtcacatatatgagaatctctagtatagttatttctcactttgctttg-gtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
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cggtacttgcatttaacgctgcaaaatatcttgatttaaattattcttgatatatgtgca---ttttgatat---ttcatgacaatttgtgttatgtctgctgcagTCTGCTATATGGAGCAGAAGACCCCTCAATTGCTGGCATGGTTCTGGATAGTGCTTTCGCTAACTTATATGACTTAATGATGGAGCTTGTAGAAGTTTAC
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
-tgttaaaatatacctcatcta-ttctatgtgtgtaattataagtcacatatatgagaatctctagtatagttatttctcactttgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
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ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttg-atggctgtcccctttaattctttacaatattttgtatacaaatgta-aatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------tgttaaaatatacctcatctattctatgtgtgtaattataagtcacatatatgagaatctctagtatagttat-ttctcactttgctttggtgcgg-------------tgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
|| | | || | || || ||||| || || | || | | | | | | | | | | | ||||| | | |||| || | || |||||||| |||||||| ||||| ||||| |||||||||||||| | || ||||| ||||||||||||| |||||| |||||||| || | ||||||||
gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagct-ttctaaaggtcta-tgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatatgagaatctctagtatagttatttctcactttgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
ttctcac putative branch site (score: 2)
tagtatagttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttaaaatatacctcatctattctatgtgtgtaattataagtcacatatatgagaatctctagtatagttatttctcactttgctttggtgcggtgtagCCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCAAACTTATATGATCTAATGATGGAGCTTGCTGATGTCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - tgtgtgt