Sequence
atgc intronic sequence ATGC exonic sequenceGTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAGgttagtacagttacattttatatgactctaccctggtaatcttgttattagagtaacatttatatttggaccatgtctagaagtagtggagtcattatgt...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g40740.2 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g40740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G100815_T01 (Zea mays), 5'ss of exon 4
GTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAGgttagtacagttacattttatatgactctaccct-------ggtaatcttgttattagagtaacatttatatttggaccatgtct-agaagtagtggagtcattatgt
|| || || ||||| ||||| || ||||||||||| |||||||||||||||||||||||||||| |||| ||||| || ||| ||||| | | | || | || | || ||| |||||| |||||| | ||| | ||| | |||
GTTCTTTACAAGCATAAGATTGTTCTATTTGGTGGCTTTTATGACACTCTTAGGGAAGTGAGgtcagtagagttaatttgtatgcaactctcatttctgatgtgctgatgtgattgcttgattaatatttatttttggatcttgtttgagagagaatgggag--------
upper sequence: LOC_Os04g40740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA06G18170.1 (Glycine max), 5'ss of exon 7
GTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAGgttagtacagttacat---tttatatgactctaccctggtaatcttgttattagagtaacatttatatttggaccatgtctagaagtagtggagtcattatgt
|| | || ||||||||||| | || |||||||| || |||||||||||||| ||||||||||| || | | | | ||| | || || | || | | || | | || | | ||| | || | | || | | || |
GTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAGgttgttaatgctgcttacttttttttgttgataattttttattgtccataattgtgttaattatatgtatgtgattttctttcccatattaaaaaaataa---
upper sequence: LOC_Os04g40740.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA04G36770.1 (Glycine max), 5'ss of exon 7
GTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAGgttagtacagttacattttatatgactctaccctggtaatcttgttattagagtaacatttatatttggaccatgtctagaagtagtggagtcattatgt-----
|| | || ||||||||||| | || |||||||| || |||||||||||||| ||||||||||| || | | | || || | | | || |||| | | | | ||| | || | | | | | | || | |
GTATTGTACAAGCACAAGATTATTCTTTTTGGTGGCTTCTATGACACTCTTAGAGAAGTGAGgttgttaatgctgc--ttgattt---tttttgttgataattatatgtatgtgattttctttctcattaaaaaaaataaaactccacagcagatgaaaagcttgccMapped 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|58611209|gb|CK038921.1|CK038921EST: CACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAG ATACTACAATGACTTACATGTTTTTGATTTAGATAATTTCAAG
genomic: CACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAGgttagtacag ... ccttctgcagATACTACAATGACTTACATGTTTTTGATTTAGATAATTTCAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCCTCTATAAGCACAAGATCGTGCTATTTGGTGGTTTTTATGACACTCTTAGGGAAGTGAGgttagtacagttacattttatatgactctaccctggtaatcttgttattagagtaacatttatatttggaccatgtctagaagtagtggagtcattatgt
- - - - - - - - - - - - - - TGGTGG