Sequence
atgc intronic sequence ATGC exonic sequence...aaatgctttgggacagttctagtcttattatcttacaatcaataatggttgtgaatctaatattcttcagaacatagtttaacgggtgaaaatattgcagTTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGGGTGGTGAAGTCTCACGCTTCATACTGGGGGGTGCCGATCTGATGTTTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g35160.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g35160.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G128189_T01 (Zea mays), 3'ss of exon 3
aaatgctttgggacagttctagtcttattatcttac-aatcaataatggttgtgaatctaatattcttcagaacatagtttaacgggtgaaaatattgcagTTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGGGTGGTGAAGTCTCACGCTTCATACTGGGGGGTGCCGATCTGATGTTTCC
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ccttgcattttgactgttttataggttttcacttactaatcaacagttgttgggcattggaaatgaattggg-tatggtttctctgctgcaaatattgcagTTTATGCGCTTTGGAAGGTCCCCCATCTGTTGCCAGCTTTTACGCTTAAAGGTGGTGAGGTTTCACGTTTCGTGATTGGTGGCGCTGATCTGATGTTTCC
upper sequence: LOC_Os02g35160.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0089g00360.t01 (Vitis vinifera), 3'ss of exon 2
aaatgctttgggacagttctagtcttattatcttacaatcaataatggttgtgaatctaatattctt-cagaacatagtttaacgggtgaa--aatattgcagTTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGGGTGGTGAAGTCTCACGCTTCATACTGGGGGGTGCCGATCTGATGTTTCC
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--atgcctgtgctttattgttaacttagaacctta-attcaattatgtcttgaaaattgacataattatcggtcctgattgtactccttttccactattgtagTTTATGCCCTCTGGAAGGTTCCTGATCTTTTGCCTGCTTTCATCCTGAAGGGGGGTGAGGTTTCTCGTTTTGTCATTGGAGGTGCTGATCTGATGTTCCCMapped 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|2310073|gb|C26228.1|C26228EST: CCCAATGCTTTTCGACATTGATGGAAGAGGCCATGAGCTGTTTCCAACAG TTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGG
genomic: CCCAATGCTTTTCGACATTGATGGAAGAGGCCATGAGCTGTTTCCAACAGgtatgtagtt ... aatattgcagTTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttgtgaatctaatattcttcagaacatagtttaacgggtgaaaatattgcagTTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGGGTGGTGAAGTCTCACGCTTCATACTGGGGGGTGCCGATCTGATGTTTCC
gtttaac putative branch site (score: 3)
aatctaatattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatgctttgggacagttctagtcttattatcttacaatcaataatggttgtgaatctaatattcttcagaacatagtttaacgggtgaaaatattgcagTTTATGCACTCTGGAAGGTTCCCGATCTGTTGCCTGCTTTTACACTTAAGGGTGGTGAAGTCTCACGCTTCATACTGGGGGGTGCCGATCTGATGTTTCC
- -tgctttg
- - - - - - - - - - - - - - - - - acaatca
- - - - - - - - - - - - - - - - - - - - - - - - - gtgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacata