Sequence
atgc intronic sequence ATGC exonic sequence...ataaaacttctgatctaaactgcactgctatgtcaaaatgatgctttactcccttttgtgctctgtaacctgaactcataaaagatttggattatgacagGCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGCTTGGGTGACCGCTATTGTGAAAATGAGGTCTATTGCATGTTGCATGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g41870.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g41870.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 7
---ataaaacttctgatctaaactgcactgctatgtcaaaatgatgctttactcccttttgtgct----ctgtaacctgaactcataaaagatttggattatgacagGCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGCTTGGGTGACCGCTATTGTGAAAATGAGGTCTATTGCATGTTGCATGCAG
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ttcatatggttcgtgg----aactccactctggtcgcagatagttttttctgttctatataagctacagttttgtgttgaacttgcaa--gatttggattgt-acagGCACGCCCATTCTTGGAGGAGTATGCAATTGACGAGCTCATAGACCCACGACTCGGAGAGCGCTACTCTGAAAATGAGGTGTACTGCATGCTGCACGCGG
upper sequence: LOC_Os01g41870.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 7
-------ataaaacttct--gatctaaactgc--actgctat--gtcaaaatgatgctt--tactcccttttgtgctctgtaacctgaactcataaaagatttggattatga--cagGCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGCTTGGGTGACCGCTATTGTGAAAATGAGGTCTATTGCATGTTGCATGCAG
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gtatgatttaagccttcttcagaccaaataacctattaatattgggcaaagtgatcttagataattttcttggtttccttttcccttttgttgcttatgttttaaaatcttattcagGCACGTCCTTTACTGGAAGAGTATGCCATTGATGAACTAGTAGACCCACGGCTGGGAAACTGTTATTCGGAGCAGGAGGTCTATTGCATGTTGCATGCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|25798254|gb|CA754215.1|CA754215EST: AGGCTGTTGACATCAACCGACCCAAGGGCCAGCAATTTTTGACTGAATGG GCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGC
genomic: AGGCTGTTGACATCAACCGACCCAAGGGCCAGCAATTTTTGACTGAATGGgttagttctt ... attatgacagGCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactcccttttgtgctctgtaacctgaactcataaaagatttggattatgacagGCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGCTTGGGTGACCGCTATTGTGAAAATGAGGTCTATTGCATGTTGCATGCAG
ctgtaac putative branch site (score: 3)
ataaaagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataaaacttctgatctaaactgcactgctatgtcaaaatgatgctttactcccttttgtgctctgtaacctgaactcataaaagatttggattatgacagGCACGCCCTTTCTTGGAGGAGTATGCAATTGATGAGCTCATAGATCCACGCTTGGGTGACCGCTATTGTGAAAATGAGGTCTATTGCATGTTGCATGCAG
- - -acttctg
- - - - - - - - -aactgca
- - - - - - - - - - - - -tgctatg
- - - - - - - - - - - - - - - - - - aatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaaa