Sequence
atgc intronic sequence ATGC exonic sequencegtacacatccatgtctgatgtctcctcctcctagctgtgaatcgccatgagagtggcacgatgagctcgatctcgccattgattgtgtttgtcagGGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGCTTCTCCTCGGCGCGGCGCGCGGGCTGGCATGCGTCCACCGGGAGTACCG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g05120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g05120.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G046201_T01 (Zea mays), 3'ss of exon 1
--------------gtacacatccatgtctgatgtctcctcctc-ctagctgtgaatcgccatgagagtggcacgatgagctcgatctcgccattgattgtgtttgtca------gGGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGCTTCTCCTCGGCGCGGCGCGCGGGCTGGCATGCGTCCACCGGGAGTACCG
|| | | | || | || ||| || | | |||| | ||| ||||| || || | ||| | | ||| || ||| ||||||||| |||||| || |||||||||||||||||||| |||| || || ||||||||||||||||| || ||| ||||||||||||||||
gtacgcgacctccgccgcaagctggttaatcacttccctcgcttgctaattgccacttgcca-gtcagtcacacgacactgtctgtcgtccgcttgtctcactcactcactcacagGTCACAAGATGTCGGGAGAGTCGGCGCTGGACTGGACGACGAGGGTGCGGCTGCTGCTGGGCGCGGCGCGCGGGCTTGCGTGCATCCACCGGGAGTACCGMapped 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|66923858|gb|CX110706.1|CX110706EST: CCTCATCTACGACTACCTCCCCAATGGCAACCTCCATGACCGCCTCCACG GGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGC
genomic: CCTCATCTACGACTACCTCCCCAATGGCAACCTCCATGACCGCCTCCACGgtacacatcc ... tgtttgtcagGGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGC
EST:
gi|58667013|gb|CK055699.1|CK055699EST: ATGACCGCCTCCACG GGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGC
genomic: ATGACCGCCTCCACGgtacacatcc ... tgtttgtcagGGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcgccatgagagtggcacgatgagctcgatctcgccattgattgtgtttgtcagGGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGCTTCTCCTCGGCGCGGCGCGCGGGCTGGCATGCGTCCACCGGGAGTACCG
cattgat putative branch site (score: 4)
attgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacatccatgtctgatgtctcctcctcctagctgtgaatcgccatgagagtggcacgatgagctcgatctcgccattgattgtgtttgtcagGGCACCGGATGTCGGGGGAGTCGCCGTTGGACTGGACGACGAGGGTGAGGCTTCTCCTCGGCGCGGCGCGCGGGCTGGCATGCGTCCACCGGGAGTACCG
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