Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcacccacctcgccagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacagGGTTGCTCCGGTGTGGGAAGAGCTGCCGGCTCCGGTGGACGAACTACCTCCGGCCGGACCTGAAGCGTGGTCTCCTGTCGGAGACGGAGGAGAAGACGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os09g23620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g23620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G169356_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------gtgagtcacccacctcgc-cagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtg--taactgaa---acagGGTTGCTCCGGTGTGGGAAGAGCTGCCGGCTCCGGTGGACGAACTACCTCCGGCCGGACCTGAAGCGTGGTCTCCTGTCGGAGACGGAGGAGAAGACGGT
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gtgagtgatcaccatataaatccggtctccctcattggccggccggcggctagctttgctttgtttttcttacacgctgccttagcctggcatgcacgccaagacgccatgaccatgaactcactcgtgcgcttgtgggtttctgaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGCGCCCGGACCTCAAGCGCGGGCTGCTGTCGGAGGAGGAGGAGAGGACGGTMapped 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
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacagGGTTGCTCCGGTGTGGGAAGAGCTGCCGGCTCCGGTGGACGAACTACCTCCGGCCGGACCTGAAGCGTGGTCTCCTGTCGGAGACGGAGGAGAAGACGGT
gtgtaac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcacccacctcgccagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacagGGTTGCTCCGGTGTGGGAAGAGCTGCCGGCTCCGGTGGACGAACTACCTCCGGCCGGACCTGAAGCGTGGTCTCCTGTCGGAGACGGAGGAGAAGACGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA