Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcacatcagtgtttatgacttgcatttatttatgattggttcacctgagttaaattgatgagtttatgttgcaaatggtttcctgatatgctcttgaatagATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAA
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49520.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49520.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G810275_T02 (Zea mays), 3'ss of exon 7
gtaagctcacatcagtgtttatgacttgcatttatttatgattggttcacctgagttaaattgatgagtttatgttgcaa--atggtttcctgatatgctcttgaatagATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAA
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----------gtaagt-ttgttggtttgtatttatctgttagaaccacacat---ttcaattgat--atttactttggaattatacaatccttg-atgctcttttttagACGCTTCGCGCTCGTGTAGCTGCTAAGGCGGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCACCATAAAAGGCTGTCCAATTTCTTAA
upper sequence: LOC_Os03g49520.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G102475_T03 (Zea mays), 3'ss of exon 7
gtaagctcacatcagtgtttatgacttgcatttatttatgattggttcacctgagttaaattgatgagtttatgttgcaaatg-gtttcctgatatgctcttgaatagATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAA
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------------gtaagttcacggcttgttttcatctgttacaactacatat---ttcaattgatatatttactttgcaatcatacaatctttgatgctcttttttagACGCTCCGCGCTCGTGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAAMapped 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|29646297|gb|CB651304.1|CB651304EST: TGCGGCAGCAAGAGCGAGAGCAAGCAATAGAGAAGCGTAAGCGTGATATG ATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTG
genomic: TGCGGCAGCAAGAGCGAGAGCAAGCAATAGAGAAGCGTAAGCGTGATATGgtaagctcac ... tcttgaatagATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttaaattgatgagtttatgttgcaaatggtttcctgatatgctcttgaatagATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAA
tcctgat putative branch site (score: 3)
tgctctt CT-rich tract
aaattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcacatcagtgtttatgacttgcatttatttatgattggttcacctgagttaaattgatgagtttatgttgcaaatggtttcctgatatgctcttgaatagATGCTGCGTGCTCGAGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTATACATGCAGTGGGCTGAGCATCACAAAAAGCTGTCCAATTTCTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG