Sequence
atgc intronic sequence ATGC exonic sequencegtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63440.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------gtaaaacatagta--ttatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaa-------ttgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
||| | | | || |||| | || | | | ||| | | ||| || ||| | | | | | | | | | ||| || ||||||||||||||||| || || |||||||| || || || || |||||||| |||||||| || || || |||||||| | |
gtatgttgtgttgatctaactggaaggaagtcatacttaaaatactacttgctaagtttatgataaataatgctagataagccttgaaagttttcaacacactggacaattcaatgttaaattgcttttctttttcacttgcccaacacattctggtgacaaaactgtatttactttaagGAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAG
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 3'ss of exon 4
------gtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaat--tgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
| ||| | || || | | | | || | || | || |||| | | || | | || |||| | |||| || ||||||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || ||| ||||||||||||| |
tatttctccgatcat--tcttctgtaatagattttaagatttt-cccaaaaaacattagttcttgacttatgaaccatgcctttgcattttatcatataccagGGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S121_20V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------gtaaaacatagtattat-ggcacaaaatctattttcttactcacttga-catggatcttcgattaaacaattgccatact--cttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
| || | | | | ||| | | | | | | | || | | |||| | | | | | | | | | | |||| || ||||| |||||||| || || ||||| |||||||| ||||||||||| ||||| ||||||||||| || || | |||||| | |
gtatgttctcctacacattaattttatctaaatttcacgttgatgcttgagatttttctctgaagaggaatcctctcaatgcaatgcttccgtgactttgcgttagggctcggcttgtggattcgatgaagacagtgttgacgacagtgtgtttacagGTGTGAATGCGGATGATGTCCGGGTAACTGTGGCTGCACCTGCAGCCCGTGGTGAAGCAAACAACGAGCTGCTTGAGTACATGGGGAAG
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S3_299V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------gtaaaacatagtattatggcacaaaatctat-tttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
|| | |||| | |||| ||| || ||| | || | | | || | | | ||||| | | ||| |||| || || ||||||||||| ||||| ||||| || ||||||||||| ||||| ||||| |||||||||||||| || | |||||||| |
gtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAG
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S3_299V6.3 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------gtaaaacatagtattatggcacaaaatctat-tttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG-----------
|| | |||| | |||| ||| || ||| | || | | | || | | | ||||| | | ||| |||| || || ||||||||||| ||||| ||||| || ||||||||||| ||||| ||||| |||||||||||||| || | |||||||| |
gtatgctgtcctgacaatcgccctctttttggtagcaacttggtgtaaccctgatgtgccaattagttcctctcatctaaatgtatattccttgattacctagcgttagtcagaattatgaaagacgccattaacaaggctatctgcacagGTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGGTGTCGCTTCA
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ36938 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
| | | || | ||||| || | || | || | | || |||| || |||||||||||||||||||||||||||||||| ||||| || | || || || |||||||| |||||||| | ||||| || |
----------------------------------gtgagtgttttcgttt---tcttccttttgagtatcagacctcctttggtgcctgctccagGAGTTAATGCTGATGATGTTCGTGTGACTGTTGCTGCTCCAGCCGCGAGAGGAGAGGCAAACAACGAACTTCTGGAGTACATGGCAAAG
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ33913 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
| | | || | ||||| || | || | || | | || |||| || |||||||||||||||||||||||||||||||| ||||| || | || || || |||||||| |||||||| | ||||| || |
----------------------------------gtgagtgttttcgttt---tcttccttttgagtatcagacctcctttggtgcctgctccagGAGTTAATGCTGATGATGTTCGTGTGACTGTTGCTGCTCCAGCCGCGAGAGGAGAGGCCAACAACGAACTTCTGGAGTACATGGCAAAGMapped 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|19878734|gb|AU239565.1|AU239565EST: TCAGGTTGCAATAGAAGTGGAAGACCGTGCACAACGTTCAGCAATCACAA GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTG
genomic: TCAGGTTGCAATAGAAGTGGAAGACCGTGCACAACGTTCAGCAATCACAAgtaaaacata ... ctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
ttgccatactcttttt CT-rich tract
attaaacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacatagtattatggcacaaaatctattttcttactcacttgacatggatcttcgattaaacaattgccatactcttttttctctctgcagGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT