Sequence
atgc intronic sequence ATGC exonic sequencegtaccatttggcctcgatccttctctctcgagcgcgagatccgcatctctctgtgtgtgtcggagtcatggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g62210.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112865_T01 (Zea mays), 3'ss of exon 1
--gtaccatttggcctcgatccttctctctcgagcgcgagatccgcatctctctgtgtgtgtcggagtca-tggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
| | ||| | || || | | | | || || || | || || | ||| |||| ||||| |||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||
gtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgc---cgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
upper sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112865_T02 (Zea mays), 3'ss of exon 1
------------------------------------------gtaccatttggcctcgatcctt--ctctctcgagcgcgagatccgcatctctctgtgtg-------tgtcggagtca-tggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
| | | || |||| | || | | | | ||| | | | ||||| || || | ||| |||| ||||| |||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||
gtaaattccgcaagcttggccgcgattactcccaacgcatctgcatgctcaggtctcgctttttaacccgcaccgacgcctgtatcctgttgctctgcgtcgccttgccgttgatctcactggatttgtctccccggcagGACGATGGTGTCGCAGCTGGTGAAGCACGAGCGCATCGAGACCACCGTTGCCAAG
upper sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 1
-gtaccatttggcctcgatccttctc--tctcgagcgcgag-atccgcat---ctctctgt-gtgtgtcggag----tcatggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
| | ||| | ||| ||| | | | | ||| | || ||| |||| | | || | || | | ||| || |||||||||||| | |||||||||||||| || || |||||||| ||||||
gtttcaattcaattataagttttccaaatcttgggtcttaccagccgtacggactgaatgtagtgtttttaaaattttcttccttattttatgccttcagAACAATGGTGTCGCAGTTGGTGAAGCACGAGCGCATTGAAACCACCGTTGCCAAG
upper sequence: LOC_Os01g62210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S194_11V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtaccatttgg-cctcgatccttctctctcgagcgc---gagatccgcatctctctgtgtgtg-------tcggagtcatggacatgtctg---ttcg------gcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
| | || || || |||| | | | | | || | | | || ||| || | |||||| | | || | | || || | |||||| | ||||||||||| ||| |||| ||||||||||||||||| || | |||
gttggcgttcgggccgtgatcactggcatttgggtgctgtgggtgggggattggcttgtatgagaggggaaccggagtaacgtacgtttttggtgtttgatgggtgcagGAATCTCGTGTCGCAGCTTGTGCAGCATGAGCGAATCGAGACCACTGTTCCTAAGMapped 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|163921230|gb|EG710458.1|EG710458EST: AAGTTCCGCAAGCTCGGCCGCCACGCCGCCCACCGAGTATCCATGCTCAG GACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGC
genomic: AAGTTCCGCAAGCTCGGCCGCCACGCCGCCCACCGAGTATCCATGCTCAGgtaccatttg ... tgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgagatccgcatctctctgtgtgtgtcggagtcatggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
tctgttc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccatttggcctcgatccttctctctcgagcgcgagatccgcatctctctgtgtgtgtcggagtcatggacatgtctgttcggcagGACGATGGTGTCGCAGCTCGTGAAGCACGAGCGAATCGAGACCACCGTCGCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC