Sequence
atgc intronic sequence ATGC exonic sequencegttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32770.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
gttaaaccctaaatatgaaaaaaaac-tctttcatttctacgaactctctat-ttctttgttctttatt-tttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| ||| || | | | | || || ||| ||| | | | | | | |||| || | | || | || || |||||||| || || || || ||| ||| ||||||||||||||||||||||||||||||||||||||||| || || ||||| ||||||||||||||||| |
----gtacgtaattaagcacacacacatcgatcaattcgatcgatttttgacatgttttgatcaatgtggcatgtgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------------gttaaaccctaaatatgaaa-----aaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtat-gcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| || ||| || ||| | | | ||| | ||| || | | | | | | || | | | ||| | ||||||| |||| || || ||| ||| || |||||||||||||||||||||||||||||||||||||| || || ||||| ||||||||| |||| || |
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaa--gctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------------------------------------gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| | | | | || | ||| | || || || || || | || || | || | | | |||||||| ||| | ||||| || || || |||||||||||||||||||||||||||||||||||||| || || ||||| | || ||||| || || |
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacg-tccatggcgctgatcatcggggttagttatcgattctgcgtgcatgcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttga--accattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
|| | | || | | | |||| | | | | ||| | | | | | | ||| | ||| | |||||||| | || | |||||||| || || |||||||||||||||||||||||||||||||||||||| || || ||||| | || ||||| || || |
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgtctatgcggccatgc-atacatgcctctgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtg-accgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
gttaaaccc--taaatatgaaaaaaaactctttcatttctacgaact--ctctatttctttgttctttatttttgaaccat-tttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| |||| | | | | | || | | ||| |||| ||| | || | || | |||| ||| | | |||||| |||| | ||||| || || || |||||||||||||||||||||||||||||||||||||| || || ||||| | || ||||| || || |
atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
------------------gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatg--caaa--------tgcagAGGAATGTAGAATCGGTTCAACGCCA------CAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
|| || || || | | | | | || | | ||| | || | | | | | | | | | | | | |||||| | || | |||| || || || || ||||||||||||||||||||||||||||||| |||||| || || ||||| | || ||||| ||
gtatgcatccatgcatatagtaggatctgtgtacgagacaca-tgcatgatcatcgtctatctcattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGTCGGGTCGTCGTCAGGCCCTCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC------
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| ||| ||| | || | || | | | || | || | || ||||||| || | ||| || | ||||||||||| |||||||| ||||||||||||||||||||||| || || || | | | || ||||| || | |
---------------------gtgatgattttttttgctcagtagctaagataattgatgagtagtgcatgtaattaattaatttg----tgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1
gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| ||| | | || | ||| | || | | | || | ||| | ||||||| || | ||| || | ||||||||||| |||||||| |||||||||||| |||||||||| || || || | | | || ||||| || ||
------------------------gtgatgatttttttgctaagtagctaaga--taattaatgagtagtgcatgtaattgattaatttgtgcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------------------gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGT---------TCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
|| ||| | | || | | || ||| | | | | || || || | | | | | | || || |||| | || || || || || | ||||||||||||||||||||||||||||| ||||| ||||| || | || | | |||||||
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcga--gccctgggattgcaattagat-tccatgtccactacgtacacggacaagtaaccccgatgtggtcat-cagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------gttaaaccctaaatatgaaaaaaa-actctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGT----TCAACGCCA-----CAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT-
|| | ||| | | | | ||| || | || | || |||| | | | | | | ||||| || || | ||| || ||| || ||||| ||| | || || | |||||||||||||||||||||||||| ||||| ||||| ||||| | | | || || || || |
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattggtggatatcttgatac--tgatgatattcaatttttgtg-gcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------gttaaacccta--aatatgaaaaaaaactctttcatttctacgaac-tctctatttctttgttctttattt-ttga----accattttggtatgcaaatgca---gAGGAATGTAGAATCGGTT-CAACGCCAC--------AAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
|| | | | ||||| ||| | | || | || | | | ||| | | || || | ||| ||||| | ||| || |||| || ||||| || | |||| | | | ||||||||||||||||||||||||||||||||| ||||| || || | | | | |||||
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------------gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctc-tatttctttgttctttatttttga-accattttggtatgcaaatgcagAGGAATGTAGAATCGGT---------TCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
|| | | ||| | || | | ||| || | | | || | || | | | |||| | | ||| | | || |||| | || || ||||| || || |||| |||||||||||||||||||||||||| ||||||||||| || || | | | | |||||
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgat-cagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
--------gttaaaccctaaatatgaaaaaaaactctttcatttctac-gaactctctatttctttgttctttatttttgaaccat----tttggtatgcaaatgcagAGGAATGTAGA-ATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| | || | | | || | | | ||| | | | | || | || ||| | | || | | | | | || | || | ||| | || ||| ||||||||||||| ||||| |||||||||||||| || ||||| | | | | |||||
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S161_73V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------gttaaaccctaaatatgaaaaaaaactctttcattt--ctacgaactc---tctatttctttgt-tctttatttttga--accattttggtatgcaaatgcagAGGAATGTAGAA-TCGGTTCAAC---GCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| || ||| |||||| | | | | ||| || ||| || | ||| | | || | ||| | | || | || | | || ||||| | |||| ||||| ||||||||||| | ||||||||||||||||||||| || | | | | |||||
gtcagtacaaactcattgcagttttttttttgtttttgtttttttaaagcaatttactcgttgaaagatatcaatagattcagaagtcagaacagagtataggatttgatcaaaaaccccacaacctgacattgaattcgactctgttcatcctcatctaaacatccgatggtctctttcatggaacagAGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACTTCTTCAGTCGCAAGGACAAGAAGTATCCAACTGGCAACCGAGCCAACCG---------
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
----------------------gttaaaccctaaatatgaaaaaaaactctttca---tttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| | | | ||||| ||||| | | | || || | | |||| || | | || ||| | | || | |||| || |||| || || || || |||| |||||||||||||||||||| |||||||| || || |||||||| ||||| ||| | || || |
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gttaaaccctaaatatgaaaaaaaactctttcatttc--tacga--actctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| | ||| | |||||| || || | | | | | | || ||| || | ||||||| ||||| | |||| ||||| ||| | ||||| ||| |||||||| ||||| |||||||||||||||||||| || || || | || ||| | || || |
---------------gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcattgttcttcgattttgg----------cagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------gttaaaccctaaatatgaaaaaaaactctttca---tttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| | | | | ||||| ||||| | | | || || | | |||| || | | || ||| | | || | |||| || |||| || || || || |||| |||||||||||||||||||| |||||||| || || |||||||| ||||| ||| | || || |
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccacacacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG
upper sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
| | ||| | |||||| || | | | | || | ||| || | || |||||| | |||| ||||| ||| | ||||| ||| |||||||| ||||| |||||||||||||||||||| || || || | || ||| | || || |
---------------gtagtctagtctcctccatttcgacatgattac-acaccactgacacctctttcattgttcttcgattttg-----gcagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
tatttctttgttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaaaccctaaatatgaaaaaaaactctttcatttctacgaactctctatttctttgttctttatttttgaaccattttggtatgcaaatgcagAGGAATGTAGAATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT