Sequence
atgc intronic sequence ATGC exonic sequenceGTATCCTTCATCTGTTTTCGTTGGTGATACCTACACCTATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcctcagttatcccttacatgttccgttattatcctttggttgtgacttaatctgtcctgtgtaatgatgcttttgctttgtctgcctgaatt...
Basic information
species | Oryza sativa |
transcript | LOC_Os07g46640.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G827205_T02 (Zea mays), 5'ss of exon 7
GTATCCTTCATCTGTTTTCGTTGGTGATACCTACACCTATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcctcagttatcccttacatgttccgttatta-tcctttggttgtgacttaa-----tctgtcctgtgtaatgatgcttttgctttgtctgcctgaatt
|||||||||| |||||| |||||||||||||||||||||||| |||||||||| ||||||||| | ||||||||||| |||||||||||||| |||| | ||||| | |||| || | || || | | || | | | || ||| | ||| || | |||| | |
GTATCCTTCAATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcgtacaaatttcactagtaattgatcatttataagtcaagagtactcatccaacatgatgtatgttgtcaattgttttct------
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G137707_T01 (Zea mays), 5'ss of exon 7
GTATCCTTCATCTGTTTTCGTTGGTGATACCTACACCTATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcctcagttatcccttacatgttccgttattatcct-ttggttgtgacttaa-----tctgtcctgtgtaatgatgcttttgctttgtctgcctgaatt
|||||| || |||||| |||||||||||||||||||||||| |||||||||| ||||||||| | ||||||||||| |||||||||||||| |||| | ||||| | |||| ||| | || || | || | | | || || | ||| || | |||| | |
GTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGgtaaacatccttaattatctcctacaagtttcactagtacttgatcatttataagtaaaaaatactcacccaacatgatgtatgttgtcaattgtttcct------
upper sequence: LOC_Os07g46640.1 (Oryza sativa), 5'ss of exon 7
lower sequence: PP1S281_35V6.1 (Physcomitrella patens), 5'ss of exon 6
GTATCCTTCATCTGTTTTCGTTGGTGATACCTACACCTATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcctcagttatcccttacatgtt----ccgttattatcctt-tggttgtgacttaatctg----tcctg---tgtaatgatgcttttgctttgt--ctgc--ctgaatt-----------------------------------------------------
|||||||||||| || || ||||||||||| |||||||||||| | |||||||| ||||| || || || || | ||||| ||||||| | | | ||| || | | ||||| || | ||| ||| | | ||| ||| | ||||| | |||| | | |||| ||| | ||||
GTATCCTTCATCAGTGTTTGTTGGTGATACGTACACCTATTTTGCGGGAATGGCTTTGGCAGTAGTAGGCATCCTTGGTCACTTCAGgtga-tgccgtcatttttgtagtcaatgtttttgccttgattgaacttgttgggctgatcgaatgcggagttcctggctttctgagatggtatcaagttgtgattgcaacccaattaagtaccactctttttggtgaaagactgacatcatccttatatggttatgcagMapped 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|38473384|gb|CF957516.1|CF957516EST: TATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAG CGAGACATTATTGCTCTTCTTTTTACC
genomic: TATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcc ... ctacttgcagCGAGACATTATTGCTCTTCTTTTTACC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTATCCTTCATCTGTTTTCGTTGGTGATACCTACACCTATTTTTCTGGAATGGCATTGGCTGTGGTGGGAATTTTGGGTCATTTCAGgtaaacgtcctcagttatcccttacatgttccgttattatcctttggttgtgacttaatctgtcctgtgtaatgatgcttttgctttgtctgcctgaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG