Sequence
atgc intronic sequence ATGC exonic sequencegtaagttaaattcaagtagtactttggaatataaatattcgttaactgggaacatttagtaacttctctcattatgcagGTATGAGCTTCACTACCAAATGATAACTTTTGGAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g29230.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g29230.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G123587_T01 (Zea mays), 3'ss of exon 6
------------------gtaagttaaattcaagtagtactttgga----atataaatattcgttaactgggaacatttagtaacttctctcattatgcagGTATGAGCTTCACTACCAAATGATAACTTTTGGAAAG
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gctagatcaacgtacattgtaagattagcccaatcaataattttcatactatattagtatatgt-agctgtctagattcaatgacgccttccaatatgcagGTATGAGCTTCACTACCAAATGATTACTTTTGGAAAG
upper sequence: LOC_Os02g29230.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G422464_T02 (Zea mays), 3'ss of exon 7
gtaagttaaattcaagtagtactttggaatataaatattcgttaactgggaacatttagtaacttctctcattatgcagGTATGAGCTTCACTACCAAATGATAACTTTTGGAAAG
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gtaagattagttcaatcgatacttttcgcactatat-----ttagatggctagattcaatgacgccttccaatatgcagGTATGAGCTTCACTACCAAATGATTACTTTTGGAAAG
upper sequence: LOC_Os02g29230.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G422464_T01 (Zea mays), 3'ss of exon 7
--gtaagttaaatt--caagtagt-actttggaata-----taaatattcgttaactgggaacatttagtaacttct--ctcattatgcagGTATGAGCTTCACTACCAAATGATAACTTTTGGAAAG-------------------------------------------------------------------------------
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gtatgagcttcactaccaaatgattacttttggaaaggtgataaacatgaaataaagaaaatgatctaacacgccctggtttactatgaactgacttgtctt-ttctctatcgtccacttttagGTTTTCTGCACAAAAAGTAAGCCTAATTGCAATTCATGTCCAATGAGAGCTGAATGTAAGCACTTTGCTAGTGCATTTGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaatataaatattcgttaactgggaacatttagtaacttctctcattatgcagGTATGAGCTTCACTACCAAATGATAACTTTTGGAAAG
tagtaac putative branch site (score: 1)
cttctctcatt CT-rich tract
tataaatattcgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttaaattcaagtagtactttggaatataaatattcgttaactgggaacatttagtaacttctctcattatgcagGTATGAGCTTCACTACCAAATGATAACTTTTGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT