Sequence
atgc intronic sequence ATGC exonic sequencegtacgttgtgcccgcgccgcgcgattgccttcctctcgtcgtcatcttctatgcgtggttggctcatggccgggcagagtgagtgaacctggtgcgtgcgtgcgtgcgggtgattttgatgtctgtctcctgcagGATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTGATCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g35590.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g35590.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064255_T02 (Zea mays), 3'ss of exon 1
gtacgttgtgcccgcgccgcgcgattgccttcctctcgtcgtcatcttctatgcgtg--gttggctcatggccgggcagagtgagtgaacctggtgcgtgcgtgcgtgcgggtgattttgatgtctgtctcctgcagGATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTGATCCAG
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--------------------gtgcgtgctgttcggccaccgctgaataagactcgggccattgtctattggacgcattgatgcattcgtttcgattgattcg-atgtgtgggt--------tgttttttttctgcagGTGTGGATTACGAGTACAAGGCGGTGAACCTTCTCAAGGGCGAGCAGTCTGATCCAG
upper sequence: LOC_Os02g35590.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G064255_T01 (Zea mays), 3'ss of exon 1
gtacgttgtgcccgcgccgcgcgattgccttcctctcgtcgtcatcttctatgcgtg--gttggctcatggccgggcagagtgagtgaacctggtgcgtgcgtgcgtgcgggtgattttgatgtctgtctcctgcagGATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTGATCCAG-------------------------------------------
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--------------------gtgcgtgctgttcggccaccgctgaataagactcgggccattgtctattggacgcattgatgcattcgtttcgattgattcg-atgtgtgggt--------tgttttttttctgcagGTGTGGATTACGAGTACAAGGCGGTGAACCTTCTCAAGGGCGAGCAGTCTGATCCAGGTGGGTTCGTACTACACCATACCATTACTTGTACTACCTACCTMapped 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|163920379|gb|EG714466.1|EG714466EST: CTGGCGGAGCTCGTGCTCGCACCGCGTCCGCATCGCCCTCAACCTCAAAG GATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTG
genomic: CTGGCGGAGCTCGTGCTCGCACCGCGTCCGCATCGCCCTCAACCTCAAAGgtacgttgtg ... tctcctgcagGATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtgaacctggtgcgtgcgtgcgtgcgggtgattttgatgtctgtctcctgcagGATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTGATCCAG
ttttgat putative branch site (score: 4)
tctgtctcct CT-rich tract
attttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttgtgcccgcgccgcgcgattgccttcctctcgtcgtcatcttctatgcgtggttggctcatggccgggcagagtgagtgaacctggtgcgtgcgtgcgtgcgggtgattttgatgtctgtctcctgcagGATTGGAGTACGAGTACAAGGCGGTGAACCTGCTCAAGGGGGAGCACTCTGATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA