Sequence
atgc intronic sequence ATGC exonic sequenceCTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31170.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g45300.1 (Oryza sativa), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
| || ||||||||||| ||||| ||||| ||||| ||||||| || ||||| || || ||||| |||||||| ||||| ||| | ||||||||||||||||| |||| | | | || | || ||| || | ||| | || || ||||||| | || ||| | || | || |
CAGACAAATCCATCAAGATAGCTGACTTTGGAGTTGCTCGAATTGAGGTACAAACTGAGGGAATGACCCCAGAGACAGGAACCTACCGTTGGATGGCACCgtaagtc--ataatca-cgcattcacgctcattgcctactgtttac---ctttttaaatctctgtcaaatatgcttatct------tgccatcatgcag----------
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g51950.1 (Oryza sativa), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaat--atctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
||| || || ||||| || || ||||| ||||| || |||||||| ||||||| ||||||||||| || || ||||| || | |||||||| |||||||||||||||| | | || | || | | | | | | | || ||||| | | || | | | || ||| |
GCGATAAATCGATTAAGATAGCAGACTTTGGAGTTGCCAGGATTGAAGTCAAAACCGAGGGGATGACACCTGAAACAGGAACCTATCGTTGGATGGCCCCgtaagttgaataaaacaactacattaatactatttaccatattatctgttagttc-tagccgcgtgcaacactttattttagttaagagaattttgtttgg----------
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g07790.1 (Oryza sativa), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
| ||| ||||| ||||||||||| ||||| || || | || ||||| |||| || || |||||||||||||| ||||| ||| | |||||||||||||||||| | |||| | | | || || ||| | | || ||||| | || || ||| | | ||| || | |||
CAGATAAATCCATTAAGATTGCTGACTTTGGAGTGGCTCGCATCGAAGTAAAAACTGAGGGTATGACACCAGAGACAGGAACCTACCGCTGGATGGCACCgtaagtt----atatattcccctgtttatttttttctc-cctgtgttatttgtatatgccaactcatgtatagcttatcacttgcaaggacttcactttag-aatg---
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g12750.1 (Oryza sativa), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag----
|| || |||||||||||||| ||||| || || || |||||||| | || || || |||||||| || || ||||||||| | |||||||| |||||||||| | | || ||| | | ||| | || | | ||| |||||| || || |||| ||||| || | ||||||| | | | |
GAGACAAATCTATCAAGATTGCTGACTTTGGAGTGGCTAGGATTGAAGTGAAGACTGAGGGAATGACACCTGAAACAGGAACTTACCGCTGGATGGCTCCgtaagttgg-catacatgctctttatcttgcttattttaatc--agtaat------tatctca--aattcgtattaagaca--atgctgttttatttttcttcactcggcatt
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G140612_T03 (Zea mays), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
|||| |||||| ||||||||||| ||||| || || || |||||||| | || || ||||||||||| || |||||||| ||| | |||||||| ||||||||||| ||| || ||| | | || | | | | | | | | ||| | ||| || || | || ||| |||||| |
GTGATAAGTCCATTAAGATTGCTGACTTTGGAGTGGCTAGGATTGAAGTCAAGACTGAGGGGATGACACCTGAAACTGGAACATACCGCTGGATGGCTCCgtaagttgatcaaacatgctctttgtcctgtttatttcaatc--agtcatcatgc-tattccaataaggcaaatctg--ttttaaattgagttatttctttttgc----
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G156013_T01 (Zea mays), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtctt-gtccttaataaccttat-atatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
|||| || |||||||| ||||| ||||| || || | |||||||| |||| || ||||||||||| || || ||||| ||| | ||||||||||||||||||||| | | | | | | | || | | ||| || || | |||| | || | ||| || ||| || | ||| | ||| |
GTGATAAATCTATCAAGATAGCTGACTTTGGAGTAGCTCGCATTGAAGTAAAAACTGAGGGGATGACACCTGAAACGGGAACCTACCGTTGGATGGCACCgtaagttgaacac-tctgacatcattagttctgcttacagatcttgttagccacacgatattaattaaaattata---agtcac-atctcatattagtatgaaag------
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G102088_T02 (Zea mays), 5'ss of exon 2
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttat-atatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
|||| || |||||||| ||||| ||||| || || | |||||||| |||| || ||||||||||| || || ||||| || | ||||||||||||||||||||| | | | | | | ||| | | ||| | | || |||| | | | || | | || || | | || | | ||
GTGATAAATCTATCAAGATAGCTGACTTTGGAGTAGCTCGGATTGAAGTAAAAACTGAGGGGATGACACCTGAAACGGGAACCTATCGTTGGATGGCACCgtaagttgaacactgacattgctggtgttacttat--taaaattagaagtcacatcatatattgaacatttatgtc-aatcaata-gtacaaaaatgtgggtca------
upper sequence: AT4G31170.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S69_199V6.2 (Physcomitrella patens), 5'ss of exon 3
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
| ||| || ||||||||||| |||||||| | ||| || || ||||| ||| ||| || ||||| |||||||| |||||||| |||||||||| |||| ||| | | || || | | || | || || || | || ||| | | | |||||| ||| | ||| | || |
CGGATAAATCTATCAAGATTGCAGATTTTGGCGCTGCTAGGATAGAAGTGCAAGTCGAGGGCATGACTCCAGAGACGGGAACTTATCGATGGATGGCTCCgtgagtattttgcaaccgatgtctttc-ccttttccctgcttttgatgatctc-tatgtttat-----ctttatttatttggtatgaacgattacaccagtttatcc--Mapped 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|124843781|gb|EH928218.1|EH928218EST: CAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACC AGAGATGATCCAGCACAGACCCTACACT
genomic: CAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaa ... atcgatgcagAGAGATGATCCAGCACAGACCCTACACT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGATCGGTCCATCAAGATTGCTGATTTTGGTGTTGCAAGAATTGAAGTTCAAACCGAAGGGATGACACCAGAGACTGGAACTTACAGATGGATGGCACCgtaagttgaataaatatctcgttttccatccttgtcttgtccttaataaccttatatatctctgcaagtcatatttagacactatattcccttattttgatcgatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA