Sequence
atgc intronic sequence ATGC exonic sequence...agtactcatttggtactagtatttgataactgaaaattacaacacatttatattgattgactctggaaatgacattatcaatatgttgagcaactttcagGCAGCACTTGAGGCACCAAGGGTTTTGAACTTAAACAGCAGCAAATATTTCTCAGGACCATATG
Basic information
species | Glycine max |
transcript | GLYMA20G36040.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36040.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G32900.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------agtactcatttggtactagtatttgat------aactgaaaattacaacacatttatatt----gattgactctggaaatgacattatcaatatgttgagcaacttt---------cagGCAGCACTTGAGGCACCAAGGGTTTTGAACTTAAACAGCAGCAAATATTTCTCAGGACCATATG
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gtaacactctttcctcttacttctgtagttacagttgtgttgtttctgaatcgtgggttctcatttgattgaaacatgtagcctacagagattaaattcataaataatgcagaatctgtgtttgaatagcgtacaagcatgagcaataacttgatttactttgatcgttggtagGCTGCTCTTGAGGCACCACAGGTTCTGAACCTGAACAGCAGCAAGTACTTCTCTGGACCATATG
upper sequence: GLYMA20G36040.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0048g02600.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------agtactcatttggtactagtatttg--ataactgaaaattacaacacatttatattgattgact-ctgga-aatgac--attatcaatatgttgagc----aactttcagGCAGCACTTGAGGCACCAAGGGTTTTGAACTTAAACAGCAGCAAATATTTCTCAGGACCATATG
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gtagttgatctctgtccttccagttgcatgaacgattttaattttgcgtaatggagacaactgcatggaacggatgggcgtaaaaatccagcttggtacaccatttactagttaattacttgttcttcacttgttcttcctatggctttcagGCAGCTCTGGAAGCACCTAGGATTTTGAATCTTAAAAGCAGTAAATATTTCTCTGGACCATATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttatattgattgactctggaaatgacattatcaatatgttgagcaactttcagGCAGCACTTGAGGCACCAAGGGTTTTGAACTTAAACAGCAGCAAATATTTCTCAGGACCATATG
gattgac putative branch site (score: 3)
ctttc putative PPT
attatcaatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtactcatttggtactagtatttgataactgaaaattacaacacatttatattgattgactctggaaatgacattatcaatatgttgagcaactttcagGCAGCACTTGAGGCACCAAGGGTTTTGAACTTAAACAGCAGCAAATATTTCTCAGGACCATATG
- - - - - - - - - - - - - - - - - - - - aacacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgag