Sequence
atgc intronic sequence ATGC exonic sequence...gatgtttgtagttagttcctattgcatgtaatattcctcttcgatcttttggtgcatttatttaaatgtttaagtaattagcgttaatttcctcaaatagAAAGGTTTGCATCGGAACAAGAACTGAGTACACATATGCACCATATCATGATGGGTACCAGTGGAGAAAATACGGGCAAAAGATGATCCGGGGCAACTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60490.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G382350_T01 (Zea mays), 3'ss of exon 1
gatgtttgtagttagttcctattgcatgtaatattcctcttcgatcttt-tggtgcatttatttaaatgtttaagtaattagcgttaat--ttcctcaaatagAAAGGTTTGCATCGGAACAAGAACTGAGTACACATATGCACCATATCATGATGGGTACCAGTGGAGAAAATACGGGCAAAAGATGATCCGGGGCAACTCC
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--cttttgct-ccacatgatgttccttgttcttatcacttgtgctattcattttgtttcttgttatgtttccaagttattaatggtcgtactttcctgagtagGAAAGTTCACATTAGCACAAGAACTCAGCACACATACGCACCGTATCATGATGGCTACCAGTGGAGAAAATACGGGCAAAAGCTGATCCGAGGCAGTACC
upper sequence: LOC_Os01g60490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G029292_T03 (Zea mays), 3'ss of exon 1
------------gatgtttgtagttagttcctattgcatgtaatattcctcttcgatcttttggtgcatttatttaaatgtttaagtaattagcgttaatttcctcaaa-tagAAAGGTTTGCATCGGAACAAGAACTGAGTACACATATGCACCATATCATGATGGGTACCAGTGGAGAAAATACGGGCAAAAGATGATCCGGGGCAACTCC
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tattttgctccacatgat-gtgcctagttcttactacttgtgctattcatttt------------gtttctggtcatgttttcaagctattaacggtgctttcgtgaaagcagGAAAGTTCGCATTAGCACAAGAACTGAGTACACATACGCTCCGTATCACGATGGCTACCAGTGGAGAAAATACGGACAGAAGATGATCCGGGGAAGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttggtgcatttatttaaatgtttaagtaattagcgttaatttcctcaaatagAAAGGTTTGCATCGGAACAAGAACTGAGTACACATATGCACCATATCATGATGGGTACCAGTGGAGAAAATACGGGCAAAAGATGATCCGGGGCAACTCC
cgttaat putative branch site (score: 4)
tttcctc CT-rich tract
atttatttaaatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgtttgtagttagttcctattgcatgtaatattcctcttcgatcttttggtgcatttatttaaatgtttaagtaattagcgttaatttcctcaaatagAAAGGTTTGCATCGGAACAAGAACTGAGTACACATATGCACCATATCATGATGGGTACCAGTGGAGAAAATACGGGCAAAAGATGATCCGGGGCAACTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- tgtttgt
- - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - -gtgcatt