Sequence
atgc intronic sequence ATGC exonic sequencegttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26510.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
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----------------------------------------------gttacatggtcacatacctttttactcactagagctgtttttatttaacatgtttacaaatcttagttgttaggtcagatctccttgatgattcttttttgaa--attaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
||| | || ||||| | | || || || |||| | | | |||| | | | | ||| || | |||| | || | || ||| | || || | ||| | | ||| | ||||| ||||||||||| |||||||||||||| |||||||| || ||||| ||||| ||||| |||||||| ||||| || ||||| |||||| |||| || |
--------------gtaacatggtcacatctattactgtttttg-----------tttttcactagttctgtttttatt-taacatgtttacaaaatattagttgttactt---gttaggtacagacttccttgatgattcatttttgaaattaacc-atttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattat-catcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttc--tcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
|||| | | | || | | | | || | |||||| ||||| | | | || | | || || | | | || | ||| || || | | | || || | | |||| || || | || |||| | || ||| ||| ||||||||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| |||||||| ||||| || ||||| || ||| |||| || |
gttacaaagcttc--ctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatc-attttttggctaataa-aacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
gttagcccgtcttagtattgttactgtatatattat-catcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
|||| | | | || | | | | || | |||||| || || | | |||| || | | ||| || || | | || || | || | ||| || | | ||||| ||| | | | || || | || |||| |||| |||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| ||| |||| ||||| || || || || ||| |||| || |
gttacgaagcttc--ctctattgcaattt-tgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaat--attcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatc--tttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
||||||| | || | | | | | | |||| || || | | ||| ||| || ||| | | | || | |||| | || ||| ||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| || || || ||||| || ||||||||||| || |
---------------------------------------------------------------------aattttaatcaagctatcattttc-tttatcagattttgatggttaata-tctaccattt---aatggatttgtgt-tgctgat-tcttatgtaatac-------ttgttgcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA-
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----------------------------------------------------------------------------aatatta-atcaagcta--tcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaata-----cttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 5
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaat-ctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
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------------------------------------------------------------------------------taacatatttcgttttttt-tatgtctaccaatattagtaattccctttttttgtttaccgtatattagtaactgtttcttataatatata-----cttgatgcagTATTCTAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTACGCTGATATCATTATACCCCGTGGAGGAGATAATCATGTGGCTA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
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---------------------------------------------------------------------------gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgctta---ccatatattagtaactgtttcttataatatata-----cttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgttttt---ttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
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------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcc---ttta-atgttaataatcct--tttatttaat--------cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 6
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttga------tgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
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-----------------------------------------------------------------------------------gaccatcccagccttgttgtccatgg--cgtcttagtgcgaacacttcgatctcgta-gcttatac--ggaatgaagatga-actaacttctggaggtgtacgcagTACGCAAAGTTTGTGAAGCCAGCGTTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGAGGAGACAATCATGTGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
ttttgat putative branch site (score: 4)
cctttt CT-rich tract
atattttatatgatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG