Sequence
atgc intronic sequence ATGC exonic sequence...catattatctactgttatgaattgatatctcataacttatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g64650.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 5
catattatctactgttatgaattgatat-ctcataacttatttttcatatgggtaaaactgc--ttgctgat-gtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
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----ttatgtgcatactttagtctctgtgcgcaaatctttgaatatatgggaatctgaccacagctactaattgtgggccctttatgatttaatattttaacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG
upper sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 4
catattatctactgttatgaattgatatctcataacttatttttcatatggg----taaaactgcttgctga-tgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
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----ttatgtgcatactttagtctgtg-cgagcaaatctttgaatatatgggaatctgacaacaattgctaactgtgggtcctttatgctgtaatattttcacagCATAAAACTATTGATAGTGTCCTGGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGTTCTGATCTAAGTGCTGCTTCTCAG
upper sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
-catatt-atctactgttatg-aattgatatctcataact---tatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
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ttttgttcatttcttcctacacaattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtt------tataaacagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAGMapped 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|218482998|gb|FG956126.1|FG956126EST: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTA CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
EST:
gi|86531269|gb|CI171475.1|CI171475EST: ACAAGTTAATGAAAATCCAGAAGGACTTGGATGAAACAAAAATTATCCTA CATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
genomic: ACAAGTTAATGAAAATCCAGAGGGACTTGGATGAAACAAAAATTATCCTAgtaagtattt ... atttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
ttctaat putative branch site (score: 2)
attgtttatgttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catattatctactgttatgaattgatatctcataacttatttttcatatgggtaaaactgcttgctgatgtgcattgtttatgttctaatatttgaacagCATAAAACTATTGAGAGTGTGCTCCAAAGAGGGGAAAGATTGGATAGCTTGGTTGAGAAGAGTTCAGACCTGAGTGCTGCTTCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT