Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaaattatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
Basic information
species | Glycine max |
transcript | GLYMA19G39080.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G54720.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaaattatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
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--------------------------------------------------------gtca-atgagaacatgattcctta-agtcttgcaaaatat-tctataatgtg--atgttttaatgcaagt--aataccaataatgtatgttgtt-------tatcctttc---tttcagATTATCCTGTCTATCACACTGCATTTGACTCCTATGATTGGATGATCCACAACGCAGATCCATTGTTTCACCGTCATGTTGCTA
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaa-attatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
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-------------------------------------------------------------------gtcaataatgttagtagtaaaatttacatcacaattaagatttcatgc--taatcaatttgg-----taaaa--tagaacttcaactttctttttcttttgtccttgagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaa-attatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
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-------------------------------------------------------------------gtcaataatgttagtagtataatttacatcacaattaagatttcatgc--taatcaatttgg-----taaaa--tagaacttcaactttctttttcttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATGACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCATGTGGCTG
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaa-attatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
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-------------------------------------------------------------------gtcaataatgttagtagtaaaatttacatcacaattaagatttcatgc--taatcaatttgg-----taaaa--tagaacttcaactttctttttcttttgtccttcagTTTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCATGTGGCTG
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaa-attatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
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-------------------------------------------------------------------gtcaataatgttagtagtaaaatttacatcacaattaagatttcatgc--taatcaatttgg-----taaaa--tagaacttcaactttctttttcttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaaattatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
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---------------------------------------------------------------------------nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatagaacttcaactttcttttttttttgtccttcagATTTTCCAGTCTATCACACTGCTTTTGACTCCTATAACTGGATGACAAACCATGGGGATCCATTGTTTCAACGTCACGTGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
ttctaat putative branch site (score: 2)
tatctttcctatttcc putative PPT
atttctaataattagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatctcatgattcactgtccagtcccagattctttaggcatatattgttttgtaatacaaaaattaaattatttctagctcaatatgccatgtctataatatgtcatatatccatggacttggatttctaataattagtgatgtaataataatatctttcctatttccagATTTTCCCGTCTATCACACTGCATTCGACTCCTATAACTGGATGGCAGAGTATGGAGATCCATTCTTCCACCGCCATGTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC