Sequence
atgc intronic sequence ATGC exonic sequence...ttgtcttcgtaaaagatgctatttcttgtcttattgacaattcttacattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
Basic information
species | Glycine max |
transcript | GLYMA04G05900.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
ttgtcttcgtaaaagatgctatttcttgtctta--ttgacaattcttacattc-ttgttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
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--ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatat--gttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
ttgtcttcgtaaaagatgctatttcttgtcttattgacaattcttacattctt-gttgagtataagctcctcatgtgagtattgaa--------tcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
|||| || || || || | | ||| ||| | ||| ||||| ||| | | ||| | | ||||| |||| ||||||||||||||||||||| || ||||||||||| ||||| ||||| ||||||| || ||| || |||| ||||||||||||||||| || ||
----cttcctaccgcat--tacttgaactgat-ttggtgattgatgaattaacagttgaatat--gttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------ttgtcttcgtaaaag-----atgctatttcttgtcttattgacaattcttacattcttgtt--gagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
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gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
upper sequence: GLYMA04G05900.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
---ttgtcttcgtaaaagatgctatttcttgtcttattgacaattcttacattcttgttgagtataagctcctcatgtgagt-attgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
| ||||| | | | | | | || ||| | | || |||| ||| | ||| | | |||| | |||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||| ||||| ||||| ||||||||||||||||||| |||| |
cattactcttccttgtattcattggtggcaatttc--tgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattg--ttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
ttcttac putative branch site (score: 2)
tctttt putative PPT
tattgaatctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtcttcgtaaaagatgctatttcttgtcttattgacaattcttacattcttgttgagtataagctcctcatgtgagtattgaatcttttagcatgcagGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - gatgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctca