Sequence
atgc intronic sequence ATGC exonic sequenceCTGAAGAAGGGTCCATGGACGGCGGAGGAGGACCAGAAGCTCGTCAGCTTCCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcacccacctcgccagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g23620.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g23620.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G126566_T02 (Zea mays), 5'ss of exon 4
CTGAAGAAGGGTCCATGGACGGCGGAGGAGGACCAGAAGCTCGTCAGCTTCCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcacc-cacctcgccagagtttcagtctctctctt--taatttggtcgatccattgatcaatggactgatgtatctg-tgtaactgaaacag-------------------------------------------
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CTGAAGAAGGGCCCGTGGTCGGCGGAGGAGGACGAGAAGCTCGTCACCTTCCTCCTCACCAACGGCCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCGgtgagtgagcgtgcctgactgaccatcccgcttccatcgtgttaattaatttggctcat--actattaggcttccatgcacgctaagacgccaacgacatgacgatgaacccactttctctctctctgtataatgggcag
upper sequence: LOC_Os09g23620.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G169356_T01 (Zea mays), 5'ss of exon 1
CTGAAGAAGGGTCCATGGACGGCGGAGGAGGACCAGAAGCTCGTCAGCTTCCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcacccacctcgccagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacag---------------------------------------------------------------------
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CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatcaccat----ataaatccggtctccctcattggcc-ggccgg--cggctagctttgctttgtttttcttacacg-ctgccttagcctggcatgcacgccaagacgccatgaccatgaactcactcgtgcgcttgtgggtttctgaatgaacag
upper sequence: LOC_Os09g23620.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv14s0006g00450.t01 (Vitis vinifera), 5'ss of exon 1
CTGAAGAAGGGTCCATGGACGGCGGAGGAGGACCAGAAGCTCGTCAGCTTCCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcac-------ccacctcgccagagtt-tcagtctctctcttt--aatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacag
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TTGAAGAAGGGACCATGGACGGCTGAAGAGGACAAGAAGCTCATCAACTTCATTCTCACCAATGGCCAATGCTGTTGGAGAGCTGTTCCTAAACTTGCAGgtctcccacattattcttatttctcttttgctaccagcttttgtctctgcaacatggaaatacgatttctaaagctgcttttcctcctgatttttttggg---Mapped 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|88585418|gb|CI703048.1|CI703048EST: CCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCG GGTTGCTCCGGTGTGGGAAGAGCTGCCGGCTCCGGTGGACGAACTACCTCC
genomic: CCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcacc ... actgaaacagGGTTGCTCCGGTGTGGGAAGAGCTGCCGGCTCCGGTGGACGAACTACCTCC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGAAGAAGGGTCCATGGACGGCGGAGGAGGACCAGAAGCTCGTCAGCTTCCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcacccacctcgccagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT