Sequence
atgc intronic sequence ATGC exonic sequencegtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52360.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 7
------------gtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgc-tcattctacgtttacatgcatgttca-tcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|| | || | ||| | | || | | | | ||| ||| | || | | | || | | | | | | ||||||||| |||||||||||| || || ||||| |||||||||| ||| ||||| || |||||||| ||||| ||||| |||||||| ||| |||
gtatacccatatgttttattttgttttaatgataatgtattaatttctcgttttcctctttgctagccttaacgagcaattttctttacttgaaatttctagATTTGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTGGATGGTCATTCAAAAGGTGTCAATTGTGTTGATTACTTCACTGGTGGTGACCGGCCATATC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 6
-------------gtgctgaaatggtctaacattgaaacatcattatggt-ttagtccgc-ttagtccgctcat---tctacgtttacatgc--atgttcatct-tcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|||| || || | | ||| || | | || ||| | |||| |||| | | | | | || | || | ||| |||||| |||| |||||||||||| || |||||||| ||| | |||| |||| |||||| || || ||||| ||||| ||||| |||||||| || || |
gtttgtgtaatctctgctttaaaagttctggttggtcacaatgttgtattatttgtcgtcattagctttttcatagtttgatggtgatatcctaatttctgtctatcagATATGGAGTCTTGGTTCCCCTGATCCAAATTTCACACTAGATGGCCATTCGAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGACCGACCATACT
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
---------------gtgctgaaa----tggtcta--acattgaaacatcattatggtttagtccgct--tagtccgctcat---tctacgtttacatgc-atgtt----catcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
| | ||| |||| ||| || ||| ||| |||| | | | || |||| | | | | | || | || || || |||||| |||| ||||||||| || ||||||||||| ||| | |||| |||| ||||| || || ||||| ||||| ||||| ||||||||| || ||
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatt-tggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 6
----------------gtgctgaaatggtctaacattgaaacatcattatggtttagtccg----cttagtccgctcattctacgtttacatgca--tgtt--catct----tcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|| | ||| | || ||| | | | || | | ||| | || | | | ||||| |||| ||||| |||||||||||||||||| || || ||||| |||||||| |||||||| |||||||||||||| |||||||| |||||||| || |||||||| || || |||
gtgtaattatgttcttgttcctggatgtttcttttttaaaaaaaaaaaaaagtaaaaagaaaaactatgatcctatgatataatgcattgatgcaactgttatcatctcttttcagATTTGGAATCTTGGCTCTCCTGACCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
gtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|| ||| | || | || | | | | | | | | | | | ||||||||||||||||||| || || || || |||||||| |||||||| |||||||||||||| |||||||| |||||||| || |||||||| || || |||
-------------gtagaattatgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctcttttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 6
--------gtgctgaaatggtctaacat-tgaaacatcattatggtttagtcc-----gcttagtccgctcatt------ctacgtttacatgc-atgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
||| | | | | | ||| | | ||||| | | | || ||| | || | ||| || || | ||||||||||||||||| || || ||||| ||||||||||||||||| ||||| |||||||| |||||||| ||||| || || |||||||| ||||| |||
gtatacatgtgttcttcttgctagttgtgtcctgcattttctttgtttatttccaaacacctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
------------gtgctga--aatggtctaacattgaaacatcattat--ggtttagtccgcttagtccgctcattctacgtttacatgc-------atgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|| || | || |||| || || | || | | || ||| | | | | || |||| | ||||||||||||||||| || || ||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| || || |||||||| || || ||
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
----------------gtgctg--aaatggtcta--acattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatg-catgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|| || || | || | |||| | || | | | || || | | | | | || | | ||| || | | | | ||||| ||||||||||| || |||||||| ||||||||| ||||||||||||||||||| ||||||||||| ||||| || || || |||||||| || |||
gtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
-----------gtgctgaaatggtctaacattgaa-acatcattatggtttagtccgcttagtccgctcattcta-cgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
|||| ||| || || ||| || || | | ||| ||| | || || | | |||||||||||||| || ||||| |||||||||||||| ||||||| ||| |||||| ||||| ||||| ||||| ||||| |||||||| ||||| || |
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctg-gcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
ttcatcttc CT-rich tract
tttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgaaatggtctaacattgaaacatcattatggtttagtccgcttagtccgctcattctacgtttacatgcatgttcatcttcagATTTGGAATCTTGGTTCCCCAGACCCAAATTTTACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG