Sequence
atgc intronic sequence ATGC exonic sequence...atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29320.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 12
------------------------atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaa--tggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
| | || || ||| || | | | || ||| | ||| | || || || || | || || | | | | |||| | ||||||||||||| |||||||||||||| || ||||||||||| ||| | ||||| || || | | |||||||| |||||||| || ||||| || || |||
gtaataatctggctacatttcagtctacagattcacagaaaaac-tctcctgcctattagaatgtagagtttttgccagactgccaactgtaagtgtttctacaaatttaa--tttcac---gcagTACTGCTGGAATGGAAGCTAGTGGAACCAGCAACATGAAGTTTGCAATGAATGGATGTATCCTTATTGGAACTTTGGATGGTGCTAATGTGGAAATCAGA
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 12
atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
| || | | | | | || ||| | || || || | | | | |||| | | | | || || | |||||||||||| ||||||||||||||||| || |||||||| ||| | |||||||||||| || | |||||||| || ||||| || ||||| || || |||
------------gtaatagtgtacct--gccactttttt------tttctctcgataggatttgtg-ttttcgttaacatcata----ttatcggttcagTACTGCTGGAATGGAAGCTAGTGGGACCAGTAACATGAAGTTTGCAATGAACGGTTGCATTCTTATTGGAACTTTAGATGGTGCAAATGTGGAAATCAGA
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G06040.1 (Glycine max), 3'ss of exon 12
atcctgacaca-aggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactttttgctggagactaagagtttctctc-tgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
||||| || | || | | || | ||| | | | || || | | | | ||||||||| || ||||||||||| ||||| || ||||| || ||||||||||||||| | ||||| || ||| | ||||||||||| || |||||||| ||||| || || ||
--aatgacatgtgagagtgagattggcactcaatgtgcattgggaaatggaatacaggtaaaacagacacactaatttatgttccctgtttctctcgtgtagTACTGCTGGAATGGAGGCAAGTGGAACTAGCAACATGAAATTTGCCATGAATGGCTGCATATTGATTGGAACTTTAGATGGGGCCAATGTTGAAATAAGG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA19G03490.1 (Glycine max), 3'ss of exon 12
-atcctgacacaaggaacaatatgtttcggttacatttatgaa-aggttataatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
| || | | || | | |||| || || || | | || |||| | || | | | ||| || ||||||||||| ||||| || ||||| || ||||| ||||||||| | ||||| || ||| | ||||||||||| || |||||||| ||||| || || ||
tgacatgtgagagtgagattggcactcaacgtgcattgggaaatgggatacaggta-caacagaaatacactaatttgtgttccctgttctgctcg-tgtagTACTGCTGGAATGGAGGCAAGTGGAACTAGCAATATGAAATTTGCAATGAATGGCTGCATATTGATTGGAACTTTAGATGGGGCCAATGTTGAAATAAGG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv14s0108g01560.t01 (Vitis vinifera), 3'ss of exon 12
---atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
| | |||| | || ||| || | | | | | || || | | | | | | | | || || ||| || || |||||||||||||| || ||||| || ||||||||||| ||| | ||||| || || | ||||||| |||||||||||||| ||||| || || ||
ttgagaatatgacaaagctaaaaatgattggtcaaaacctgttggtagtcatca--agtagtgttggagtctaaatatagcttttatctgtctcttact-tagCACTGCTGGGATGGAGGCCAGTGGAACCAGCAACATGAAGTTTGCAATGAATGGCTGTATCCTGATTGGGACCTTGGATGGGGCCAATGTTGAAATAAGG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S53_212V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------atcctgacacaaggaacaatatgtttcggttacatttatgaaaggtta--taatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
| | | | | | || | | | | || | | ||| || | | || || | | | || | ||| | | |||||||||||| || |||||||| ||||| |||||||||||||| || || ||||| || || || |||||||| || ||||| || || ||||||||||||||
gtatagagttgcaaaaatcggcagaccgtaat-cttgattttatctactcctggtaggtaccagcttggtagattagtgagtgatgatcgtgtctgaccccat-gattgaga---tgtgactgcagTACTGCGGGAATGGAAGCCAGTGGAACAAGCAACATGAAGTTCTCAATGAATGGGTGTGTCTTGATTGGCACTTTGGACGGTGCAAATGTCGAGATTAGG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S86_213V6.1 (Physcomitrella patens), 3'ss of exon 11
------------atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcat-------actttttgctggagactaagagttt-ctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
| || || ||| ||| || | || ||| || || ||||||| || || | | | || | | ||| | | || | | ||||| || || ||||||||||||||||| || ||||||||||| || | |||||||| ||||| ||||||||||| ||||||| || || || ||||| ||
gtgacaacgaaggactatactcacggactaatcagtctta-ttgcatctac-aatcaccataatcagcatcagtctttgaaatcagatcttacagaagaaaattatcttgcattgtgcagCACGGCAGGGATGGAAGCTAGTGGAACGAGCAACATGAAGTTCGCCATGAACGGCTGCGTGCTGATTGGAACCCTGGATGGAGCCAACGTTGAGATCCGA
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S195_41V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------------------------------atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactt------tttgctgg---agactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
|| || | | || | ||| || || | | | || || | | || | ||||| | | | | || | | ||||||||| || |||||||| ||||| || || |||||||| ||||||||||| || || || |||| || || ||||| || || ||||||||||| |
gtacatcttttcacctgcaaactcctcatcctgtatctgttacattccagtgtgtctcttaggccactgttgatgagattttattttatattttgttttatttatttatttattttccttcttcttcttcttcttcttcttcttctagacacttgattgcggtgtgtgctgatccatgttgtgtggtttggttt-cagTACTGCGGGAATGGAAGCAAGTGGCACGAGTAACATGAAGTTTTCGATGAATGGATGTGTCCTGATCGGCACTTTGGACGGTGCCAATGTCGAGATCCGG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ09932 (Selaginella moellendorffii), 3'ss of exon 11
atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactttttgctggagactaagagtttctctctg------cagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
|| | | || | ||| | || || | || | | ||| | || ||||| || || |||||||||||||| || |||||||||||||| ||||||||||| ||||||||||| || | ||||| || || |||||||| |
---------------------------------------------gtacataccatt-cgctcttttcttctgtttgaactggatatcttccttttgatgatgtagTACGGCGGGAATGGAAGCTAGTGGAACCAGCAACATGAAATTCTCGATGAACGGAGCTGTTTTGATTGGCACTCTCGATGGTGCCAACGTCGAGATCCGCMapped 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|124989010|gb|EL061357.1|EL061357EST: AGTGTTGCTGAATTGCTCATTCCAGCAAGTGAGCTTTCTCAGCACATCAA TACTGCTGGGATGG
genomic: AGTGTTGCTGAATTGCTCATTCCAGCAAGTGAGCTTTCTCAGCACATCAGgtaaaaactt ... ctctctgcagTACTGCTGGGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
tttctctctgc CT-rich tract
atacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcctgacacaaggaacaatatgtttcggttacatttatgaaaggttataatcaatggcactcatactttttgctggagactaagagtttctctctgcagTACTGCTGGGATGGAAGCTAGTGGGACAAGCAACATGAAATTTTCGATGAACGGTTGCGTTTTGATTGGAACCTTGGATGGGGCGAATGTCGAGATTAGA
- - - acacaag
- - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - taatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agactaa