Sequence
atgc intronic sequence ATGC exonic sequencegtaaaataatcatttacactgttgataatttctacattgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA05G32070.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 5
gtaaaataatcatttacactgttgataatttctacattg---taattttaatg---aatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
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-----------gtaaataccatcagttagttagacatggacctaatttacatgttcagtgttcaggatttcttatggattcctaacattaatt-tagGTGCATTTGCTATATACTTGGAGCCTTGGCATGCTGATATTTTTGAGTTCCTTGATTTAAGAAAGAACCATGGAAAG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 5
----gtaaaataatcatttacactgttgataatttctacattgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
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gtaggttctatggtcaattttatttgtgaaaattactctaataccat-------aatctccaggaattctcataccctcctaaaaatc-----agGTGCATTTGCTGTGTACTTGGAGCCTTGGCATGCGGATATTTTTGAGTTCCTTGATCTGAGAAAGAATCATGGGAAG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 5
gtaaaataatcatttacactgttgataatttctacattgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
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-----gtatgtttcttcattatcgtcgcttttagttccttcatcttcagaaattctaacgagct--tctaaaaactt------------agGTGCATTTGCTGTATACTTGGAGCCTTGGCATGCTGATATTTTTGAGTTCCTTGATCTGAGAAAGAACCATGGGAAG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 5
gtaaaataatcatttacactgttgataatttctacattgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
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---gtatgctttttttcattatttccacttttagtaacatcgtcttcagaaattcttatgagct-tctaaaactt--------------agGTGCATTTGCTGTATACTTGGAGCCTTGGCATGCTGATATTTTCGAGTTCCTTGATCTAAGAAAGAACCATGGGAAG
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 5
gtaaaataatcatttacactgttgataatttctacattgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgta----gGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
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---gtacaatcattaaaccttgctttattttgctgagggtaatgttcaaaaat-ttgattgtgccttgtgtaaatgtgataatctctgcatacagGTGCTTTTGCTGTGTACTTGGAGCCATGGCATGCTGACATATTTGAGTTTCTAGATCTTAGGAAAAACCATGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
ttttaat putative branch site (score: 3)
tgtttctt putative PPT
attttaatgaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaataatcatttacactgttgataatttctacattgtaattttaatgaatatttataaattgtcttgcacattttgtgtttcttgtagGTGCATTTGCTGTGTACCTGGAGCCATGGCATGCTGATATATTTGAATTCTTGGATTTAAGGAAAAACCATGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA