Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G02890.1 |
| intron # | 22 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
-gtatgttgctagacgttaagaacagctctcatac--ctgtttattacagttcc--tttttctttctgaatatctt---ttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | || ||| | || | || | | | || | || ||| || | ||| | |||| || | || || ||||||||||| |||||||||| ||| | ||||| ||||| ||||||||||||||||| |||||||| || || || ||| |||| ||||| || | | ||||
tgtgaatcactcttttttat-attgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgt--ttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggat-caaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||||| | | | | | | | | | | |||| || || || || ||| | || || ||| ||| | |||||||||| ||||| ||||| | ||||||||||| || |||||||| ||||| |||||||| |||||||| ||| | || ||||| || |||||||| |
gtatgct--tgagcatgtgggttggttttattgtc-----atta--gtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
----gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||| ||| | | || ||| | | | || | | ||| || | |||||| | | | || | ||||||||| ||||| |||| || ||||| || || |||||||||||||| |||||||| ||||| || || || ||| | |||||||| || || | ||||
gtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatg--tttgctttctagtttatcttcttcatcttgt----gttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
gtatgttgctagacgttaagaacag-ctctcat-acctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||| | || || ||| | | || || | || ||| ||| | || | || |||| | || ||| ||||||||| |||||||||| ||||||||||||||||| |||||||| || ||||| |||||||| || || || ||| | |||||||| || | | ||||
----gttagt-gattttcttaacggtcactgatgatatgcctatgaca----taataagttgtagcttactcattgatttgtgtcctgtatat-tagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
-----------------------------------------------gtatgttgctagacgttaagaacagctctcat--acctgtttattac-agttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| ||| | ||| | || | || | | | | || | | | | || | | || | | || | | | | || | ||||||||| ||||||||||||| || ||||| || |||||||||||||| |||||||||||||| || || || ||| | |||||||| || | | ||||
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccac-aatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttt-tagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
-------------gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | | |||| | | | | | | | || | || ||| || | | | | || | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || | | ||||
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccga--ggaggtgggaggctttcctgctcatttatcctgc-----ccttgtttt-tagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttt-tctttctgaatatcttttgaacgg--gatcaaaattatg----tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | || ||| || ||| | | |||| |||| || || | | | || || ||| || ||| || ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || | | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtatgttgctagacgttaagaacagc-tctcatacct-gtttatta-cagttcctttttctttctgaatatcttttgaacgggatcaaaatta---tgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | || ||| || ||| | | ||| | |||| || || | || | || | | | | || | | | | | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || | | ||||
gtacgtactggtctaattaaaggtgcatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatatgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtatgttgctagacgttaagaacagctctcatacctgt---ttatta-cagttcctttttctttctgaatatcttttgaacgggatcaaaatta---tgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | || ||| || ||| | | |||| |||| || || || | || | || | | | | || | | | | | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || || | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagcattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtatgttgctagacgttaagaacagctctcatacctgt---ttatta-cagttcctttttctttctgaatatcttttgaacgggatcaaaatta---tgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | || ||| || ||| | | |||| |||| || || || | || | || | | | | || | | || | | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| | | | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttattctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGATCTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 2
----------------------------------------gtatgttgctagacgttaagaacagctctcatacctgtttatta-cagttcctttttctttctgaatatctt-----ttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||| | | | | || | | | |||| || || |||| | || | | | | |||| || | | | | | || | |||||||| ||||||||||||| | ||||| || ||||||||||||| ||||| |||||||| || || | ||| | |||||||| || | | | ||
gtaagttatagtagtgttgtgattcatgtacattttctacttatttcaattgtactaggacaccaccatatttgtagtttgttgtcaattccatattgatgcatactttcttgctcatttatcatgccctagttttt--agGTTGATGGCATGCTGGGAAGGCAGGAGAACCCTAGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTCTATGGTGAACTGGGATGGTCTCAGAAGAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | | | || | | | | | | ||| | | | | | | | | |||| | | || || |||| ||||| ||||| ||||| | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || || | ||| |
--------gtatgcaagcacacaagtttactttagtaatcactaccggcacagtatataccaacttcttttttt-------ttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
gtatgttgctagacgttaagaacagctctcatacctgtt-tattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | || || || ||| |||| | | || | | | | | | | | | || || |||| ||||| ||||| ||||| | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || | ||||| |
-------------------gtat-gcaagcagacaggttacattagtaaacactgttggtac--agtgtacaccaactgtctttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatc--aaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | || || || ||||| | ||| | | | | | ||| | | | | || || |||| ||||| ||||| ||||| | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || || ||||| |
-------------------gtat-gcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 19
--gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatct---tttgaacgggatcaaaattatg----tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | ||| || | || | | | ||||| | | || ||||| | ||||| ||||| | | | || |||||||||| ||| | ||||||||||| ||||| || |||||||| ||||||||||| |||||||| ||||||||| | || ||||| || || | ||||
aaatgagcattcagaatctag---tgtttttctttggtagcttctacagatattcttgctttc-aattatctgtgtttgatttgttttgtgacattggtggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAACATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGAGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
-----gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatg-tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | | | | | || | || || | || ||| | || | | | ||| | | | | ||| |||||||||| ||| | ||||||||||| ||||| || || ||||| ||||||||||| |||||||| ||||||||| | || ||||| || || || ||||
ggcttaaacatattcaaatctagtgtttttctttggtagct-tctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
upper sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
-------------------------------------------------------------------------------------gtatgttgctagacgttaagaacagctctcatacctgtttattacagt-tcctttttctttctgaatatcttttg--aacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||| | | | || | || | | || || | | | ||||| || | || || | ||| ||| | | | ||||||| |||||| | || |||||||| |||||||||||||||||||||||| | || |||||||| || |||||| | |||||||| ||| |||| ||||
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAAMapped 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|125148436|gb|EL182107.1|EL182107EST: TTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG GTTGATAGCATGCTGGGAAGACGTGAGAATCC
genomic: TTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAGgtatgttgct ... aattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
atcaaaattatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
