Sequence
atgc intronic sequence ATGC exonic sequencegtgttttttctgatctcttgatatgtagtattgtttttaattcaacattgtatcccgcttatatgctctgtttggatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACTTATGGTGCAGTTTACCATGGTAAATGGAGAGGATGTGATGTTGCTATTA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g54510.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 2
gtgttttttctgatctcttgatatgtagtattgtttttaattcaacattgtatcccgcttatatgctctgtttggatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACTTATGGTGCAGTTTACCATGGTAAATGGAGAGGATGTGATGTTGCTATTA
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---------------gtatgttatgtgatctctgtgtgaattttactttatgtttcatttata--ctgtttatggatcatgcagACTATAAAAAATGACGATTTGGAGGAAATTAGAGAGCTGGGTTCAGGTACTTATGGGGCAGTTTATCATGGTAAATGGAGAGGATGTGATGTCGCTGTTA
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 1
gtgttttttctgatctcttgatatgtagtattgtttttaattcaacattgtatcccgcttatatgctctgtttggatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACTTATGGTGCAGTTTACCATGGTAAATGGAGAGGATGTGATGTTGCTATTA
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gtatgtttagtgatctcttgttgtgtagtactgtttg-aattttacattatgttccatttataa--tctgtatggatcatgcagACTATAAAAAATGATGATTTAGAGGAAATTAGAGAGCTGGGTTCAGGTACTTATGGGGCGGTCTATCATGGTAAATGGAGGGGATGCGATGTTGCTATTA
upper sequence: LOC_Os02g54510.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------gtgttttttc-tgatctcttgata--tgtagtattgtttt--taattca-acattgtatcccgcttatatgc------tctgtttggatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACTTATGGTGCAGTTTACCATGGTAAATGGAGAGGATGTGATGTTGCTATTA
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gttctcgaccaatatacaccattatttttgtaaaacatctctttggaaatcacacctttatctcttcattatctcttctccatcttagtgtctttttactatttcatgcattttatttcctctgcctaactcgaatttgtgttctttctttagACAATAAAAAATGATGATCTGGAGGAGATTCGGGAATTAGGTTCTGGTACGTATGGAGCTGTTTACCATGGAAAATGGAAGGGGTCTGATGTAGCAATAAMapped 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|29677568|gb|CB673843.1|CB673843EST: GAATTGAGGCTACAACCGCTGAAGCAGAAGCTTTATCAAAAGGACTACAG ACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACT
genomic: GAATTGAGGCTACAACCGCTGAAGCAGAAGCTTTATCAAAAGGACTACAGgtgttttttc ... gatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtttttaattcaacattgtatcccgcttatatgctctgtttggatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACTTATGGTGCAGTTTACCATGGTAAATGGAGAGGATGTGATGTTGCTATTA
ttttaat putative branch site (score: 3)
ttttaattcaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttttttctgatctcttgatatgtagtattgtttttaattcaacattgtatcccgcttatatgctctgtttggatcatgcagACTATAAAAAATGATGACTTGGAGGAAATTAGGGAGCTAGGTTCAGGTACTTATGGTGCAGTTTACCATGGTAAATGGAGAGGATGTGATGTTGCTATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG