Sequence
atgc intronic sequence ATGC exonic sequence...atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G02890.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
-atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcc--tttttctttctgaatatctt---ttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||| | | | | || | || | | | || | || ||| || | ||| | |||| || | || || ||||||||||| |||||||||| ||| | ||||| ||||| ||||||||||||||||| |||||||| || || || ||| |||| ||||| || | | ||||
tgtgaatcactcttttttatattgcctatgattc----agcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgt--ttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 23
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggat-caaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||||| | | | | | | | | | | |||| || || || || ||| | || || ||| ||| | |||||||||| ||||| ||||| | ||||||||||| || |||||||| ||||| |||||||| |||||||| ||| | || ||||| || |||||||| |
-----gtatgct--tgagcatgtgggttggttttattgtc-----atta--gtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 23
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| ||| ||| | | || ||| | | | || | | ||| || | |||||| | | | || | ||||||||| ||||| |||| || ||||| || || |||||||||||||| |||||||| ||||| || || || ||| | |||||||| || || | ||||
-gtaagtaaattgtaattgatcaatcacaacgcctttctgaattccctgtgatg--tttgctttctagtttatcttcttcatcttgt----gttgtatagGTTGATGGCATGTTGGGTAGGCGTGAAAACCCTGGAGAACATGAAGCAATGCGTAAAATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
atgaggtatgttgctagacgttaagaacag-ctctcat-acctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
||| | || || ||| | | || || | || ||| ||| | || | || |||| | || ||| ||||||||| |||||||||| ||||||||||||||||| |||||||| || ||||| |||||||| || || || ||| | |||||||| || | | ||||
---------gttagt-gattttcttaacggtcactgatgatatgcctatgaca----taataagttgtagcttactcattgatttgtgtcctgtatat-tagGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 18
------------------------------------------atgaggtatgttgctagacgttaagaacagctctcat--acctgtttattac-agttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | | ||| | ||| | || | || | | | | || | | | | || | | || | | || | | | | || | ||||||||| ||||||||||||| || ||||| || |||||||||||||| |||||||||||||| || || || ||| | |||||||| || | | ||||
gtaagttatagtagtgttgtgatccatgaacaatttctatttatttgatctgtaccaggacaccac-aatatctgtagtttgtcaatcccgtattaatgcatacttttctgctcatttatcctgctcttgtttttattttt-tagGTTGATGGCATGCTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGTAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G168228_T01 (Zea mays), 3'ss of exon 2
------atgaggtatgttgct--agacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | || || |||| | | | | | | | || | || ||| || | | | | || | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || | | ||||
acttactccacctctgggactttgaacgtccaatgtggagagcctggcagccga--ggaggtgggaggctttcctgctcatttatcctgc-----ccttgtttt-tagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G409190_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttt-tctttctgaatatcttttgaacgg--gatcaaaattatg----tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| || | || ||| || ||| | | |||| |||| || || | | | || || ||| || ||| || ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || | | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcctatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCGGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G370521_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------atgaggtatgttgctagacgttaagaacagc-tctcatacct-gtttatta-cagttcctttttctttctgaatatcttttgaacgggatcaaaatta---tgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| || | || ||| || ||| | | ||| | |||| || || | || | || | | | | || | | | | | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || | | ||||
gtacgtactggtctaattaaaggtgcatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccaccatatatgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G417650_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------atgaggtatgttgctagacgttaagaacagctctcatacctgt---ttatta-cagttcctttttctttctgaatatcttttgaacgggatcaaaatta---tgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| || | || ||| || ||| | | |||| |||| || || || | || | || | | | | || | | | | | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| || || | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagcattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttatcctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTAAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G482077_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------atgaggtatgttgctagacgttaagaacagctctcatacctgt---ttatta-cagttcctttttctttctgaatatcttttgaacgggatcaaaatta---tgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| || | || ||| || ||| | | |||| |||| || || || | || | || | | | | || | | || | | ||||||||| ||||| ||||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||| | |||||||| | | | ||||
gtacgtactggtctaattaaaggtacatactgtcttgcttgctatgcttgtggacgaggtaagttatagtattgttgtgattcatgaacattttctgtttatttctactgtaccaggacaccac-catatctgtagtttgttgtcaatcccatattgatgcatactttcctgctcatttattctgcccttgtttttagGTTGATGGCATGTTGGGAAGGCGGGAGAACCCTGGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTTTATGGTGAACTGGGATGATCTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G438355_T01 (Zea mays), 3'ss of exon 2
-------------------------------atgaggtatgttgctagacgtta--agaacagctctcatacctg---tttatta-cagttcctttttctttctgaatatctt-----ttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| || | | | || || ||| | | |||| || ||| || || |||| | || | | | | |||| || | | | | | || | |||||||| ||||||||||||| | ||||| || ||||||||||||| ||||| |||||||| || || | ||| | |||||||| || | | | ||
gtaagttatagtagtgttgtgattcatgtacattttctacttatttcaattgtactaggacaccac-catatttgtagtttgttgtcaattccatattgatgcatactttcttgctcatttatcatgccctagttttt--agGTTGATGGCATGCTGGGAAGGCAGGAGAACCCTAGAGAACATGAAGCCATGCGGAAGATGAAAAATGAGTCTATGGTGAACTGGGATGGTCTCAGAAGAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 3
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
|| | | | || | | | | | | ||| | | | | | | | | |||| | | || || |||| ||||| ||||| ||||| | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || || | ||| |
-------------gtatgcaagcacacaagtttactttagtaatcactaccggcacagtatataccaacttcttttttt-------ttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCACACTA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 14
atgaggtatgttgctagacgttaagaacagctctcatacctgtt-tattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | || || || ||| |||| | | || | | | | | | | | | || || |||| ||||| ||||| ||||| | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || | ||||| |
------------------------gtat-gcaagcagacaggttacattagtaaacactgttggtac--agtgtacaccaactgtctttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 8
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatc--aaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | || || || ||||| | ||| | | | | | ||| | | | | || || |||| ||||| ||||| ||||| | || |||||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||| || || ||||| |
------------------------gtat-gcaagcacacaagtttactttagtaaccactaccggcacagtatataccaactttttttttgactttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGGTTGCGCACTA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 19
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatct---tttgaacgggatcaaaattatg----tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | | ||| || | || | | | ||||| | | || ||||| | ||||| ||||| | | | || |||||||||| ||| | ||||||||||| ||||| || |||||||| ||||||||||| |||||||| ||||||||| | || ||||| || || | ||||
---aaatgagcattcagaatctag---tgtttttctttggtagcttctacagatattcttgctttc-aattatctgtgtttgatttgttttgtgacattggtggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAACATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGAGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
--atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatg-tagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
| | || || | | | | || | || || | || ||| | || | | | ||| | | | | ||| |||||||||| ||| | ||||||||||| ||||| || || ||||| ||||||||||| |||||||| ||||||||| | || ||||| || || || ||||
ggcttaaacatatt--caaatctagtgtttttctttggtagct-tctacggatattcttagtttcaattatctgtgtttgatttgctgtgttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA
upper sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
-------------------------------------------------------------------------------atgaggtatgttgctaga--cgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttg--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|116386258|gb|EG428850.1|EG428850EST: AGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAG GTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATG
genomic: AGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAGgtattgatca ... aattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATG
EST:
gi|116386261|gb|EG428853.1|EG428853EST: AGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAG GTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATG
genomic: AGGCTGGGGCAAACTTTATCAATATTTCAATGTCCAGCATTACTTCAAAGgtattgatca ... aattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - aagaaca
- - - - - - - - - - - - - - - - ctcatac