Sequence
atgc intronic sequence ATGC exonic sequencegtatgatcagtagttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g57710.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g57710.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116670_T01 (Zea mays), 3'ss of exon 3
--------------------------------------gtatgatcagtagttttctgtcgagtccatg---attcatgcagtagcatt--accatcc-------ttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
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gtcgtacggtacacaacaacgacgccccgggcattcgcgttcctccctaatgttgctgcaaagtccatatatataggtaccgtaccagtgaatcattcaattctatgtatctgcagACCGCGGCAGCGACGTCTTCGTTCATGGTCCTGTTCTGTGCGTCCATGTCCATGGTCCAGTTCATCCTGCTGGGCGTGGAAGGCGTCGGGCAGGCCTGCG
upper sequence: LOC_Os01g57710.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116670_T02 (Zea mays), 3'ss of exon 3
------------------------------gtatgatcagtagttttctgtcgagtccatg---attcatgcagtagcatt--accatcc-------ttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
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gtacacaacaacgacgccccgggcattcgcgttcctccctaatgttgctgcaaagtccatatatataggtaccgtaccagtgaatcattcaattctatgtatctgcagACCGCGGCAGCGACGTCTTCGTTCATGGTCCTGTTCTGTGCGTCCATGTCCATGGTCCAGTTCATCCTGCTGGGCGTGGAAGGCGTCGGGCAGGCCTGCGMapped 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|87028175|gb|CI111869.1|CI111869EST: AGATTCGTAAGCTACTGAAACTATGGTCCTATGGACCTATGGTTACCAAG ACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
genomic: AGATTCTTAAGCTACTGAAACTATGGTCCTATGGACCTATGGTTACCAAGgtatgatcag ... tgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
ccttgat putative branch site (score: 5)
ccatcctt CT-rich tract
ttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatcagtagttttctgtcgagtccatgattcatgcagtagcattaccatccttgatttgcagACTGCAGCAGCGACGTCTTCGTTTATGGTCCTTTTCTGCGCATCCATGTCGATGGTTCAGTTCATCCTGCTAGGCATGCAAGGCATCGGAGAAGCTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC