Sequence
atgc intronic sequence ATGC exonic sequencegtttttcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62040.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 7
gtttttcagtttctgattga-gcggcacccattctttgaaactggattaaattta-atgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
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gttttcttctttttgactaccattttttttagtttcttaggcagtatcaaatttggataaccatataagaattttcagctggtttttaat-tttatatga-----tgacagGTGGTAAATAGATATATCGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 6
gtttt---tcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaa--cattccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
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gttttgattttttttttcagctaactttttttagttttataggcagtatcaaattttatataatcatgtaagaatcttcacctgattttaaatttt------acatggtgaaagGTGGTAAACAGATATATCGACGAAGGAATCGCAGAGCTTGTACCTGGTGTTTTGTTCATTGATGAG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 6
gtttttcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaacat-tccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
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------taaagtcatacccatgagttctgaccagaaaaaaccaaaggaaaaaagaaaagaaggtacaatataaaaacaagagggtaactgtttttgttgg----tggcagGTTGTTAACCGATATATTGATGAAGGTGTAGCAGAGCTTGTTCCTGGAGTTCTATTCATTGATGAG
upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 6
gtttttcagtttctgat--tgagcggcacccattctttgaaactggattaaatttaatgaacat-tccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
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-----taaagtcatactcatgagttgtgtccagaa---aaaaccaaaggaaaaaagaaaaggaggtacaatataaaaataagagagtaactgtttttgttgg----tggcagGTTGTCAACCGATATATTGATGAAGGTGTAGCAGAGCTTGTTCCTGGAGTTCTATTCATTGATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
ctttaat putative branch site (score: 4)
tttaatctttatattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttcagtttctgattgagcggcacccattctttgaaactggattaaatttaatgaacattccaggatcgatgtatgatctttaatctttatattgcattttagtagGTGGTCAACAGATATATTGATGAAGGAATTGCAGAGCTTGTACCTGGTGTTCTGTTCATTGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT