Sequence
atgc intronic sequence ATGC exonic sequencegttagtagcaaagtgatttaaagtttttcttgacatatcacttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17890.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 3'ss of exon 5
------------------------------gttagtagcaaagtgatttaaagtttttctt-------------gacatatcacttctttgatctaaccattatgt------aacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
| | || | ||| || || | || ||| |||||| || ||| | | |||| | | | | |||||| ||||||||||| ||||| ||||| ||||| || ||||||||||| ||||| |||||||| |||| || ||||| |||||||| ||||| || || ||
gtatttatttcaagagcttttgcttatgtgcatctttgctatgtgcttccaattgttgcttctgatttgagtaggacata-caagtctgcagttcattcattgttttctttcattactgtagGGAAAAAGTTTCACGATATAGTTGGCAGTGCCTATTATGTAGCACCAGAAGTTTTAAAACGACGGTCTGGCCCTGAGTCAGATGTTTGGAGCATAGGAGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 4
--------------gttagtagcaaagtg---atttaaagt-ttttcttgacatatcact--tctttgatctaacc---attatgtaacaatgt----agGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
|| || | || ||||| |||||| | | | | | | | | ||| |||| || | ||| ||| | |||| ||| |||||||| ||||| |||||||||||||| |||||| | || |||| ||| || || ||||| || || ||||||||||| ||
aaatgaaggatacgactaacttttgagggcaaatataaagaattttctcaataaagaaattattctcagtgtaattgaaattaagttgccgcactcacagGGAAACACTTTCGTGACATTGTTGGAAGTGCCTACTATGTAGCACCAGAAGTGCTTAAGCGTAAGTCAGGCCCAGAATCTGACGTTTGGAGTATTGGCGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatcacttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
|||| || | | || | |||| |||| || | || | |||| || || |||| ||| ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||||| ||| || ||| |||||||||||||||||||||||||
gtgagggaaagtcttgatttttgtggtcaatttctttctttttcttttcttccattttttgtttcaggcttgttctcctatttcttcagttgagttatcaggcatgctcttgccatttttatttgagatttgtttttctctatct-----ttgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGTAAGTCTGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatcactt----ctttgatctaaccat-tatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
| | | ||| || || | ||||| || | | || || | | | || | || |||| ||| ||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| | ||| || ||| |||||||||||||||||||||||||
gtgagggaaagtcttgattttcatgctcaatttctttatttttcttttcttccattttttgttgcaggcttgttctatttctttggttgagttatc-aagcatgctcttgtaattttatttgagatttatttttctctatctgaaaaaaaatgcagGAAAAAAGTTTCATGATATTGTTGGCAGTGCTTACTATGTTGCACCTGAAGTGTTAAAACGCAAGTCAGGTCCTCAATCAGATGTGTGGAGTATTGGTGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 6
--------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatcactt---ctttgatctaaccattatgtaa-caatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
||| ||| ||| | || | | | | || | || | | | | || || ||| ||| || | |||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||||| ||| || || || || ||||| ||||||||||||||
gtgagcaaaaatgtgttgatcattatctttgtttcctttttatccctcttagcattcaaaatgttcttgcaatctttatttgagttatggttttctctctttgcaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGTAAGTCAGGTCCCGAGTCGGATGTATGGAGTATTGGTGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 6
--------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatc--------acttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
|| | | || || || | |||||| || | | || |||| ||| | || ||||| ||| || | |||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||| | ||| || || || |||||||| ||||||||||||||
gtgagcaaaaatatgtgttaatcgttattttgttccctttttatccctctttgcattcaacatgttcttgcaatctttatttgagagttatttgttctctctctttgaaaacaaaacagGAAAGAGGTTTCAAGATATTGTTGGCAGTGCTTACTATGTTGCACCAGAAGTGTTAAAACGAAAGTCAGGTCCCGAGTCAGATGTATGGAGTATTGGTGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------gttagtagcaaagtgatttaaagtttttcttgacatatcacttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
| || | | | ||| | | | | | | || || | | |||| | || ||| || |||||||| ||||||||||| ||||| |||||||| || |||||||| || | ||| | |||||||||||||||||||| ||||||||||||||
gtaagtgaaatttcgccttctcaatatatggactttgaaatccatattttcatgggtttctgttgttcaaacaattacaacatatgcttctagcttttgaattggaaaaactgaatatgaataaacacagGGAAGAAGTTTCAAGATATTGTTGGTAGTGCCTACTATGTTGCTCCTGAAGTATTGAGACGGAAATCGGGACCTGAATCAGATGTCTGGAGTATTGGTGT
upper sequence: AT2G17890.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S199_57V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------gttagtagcaaagtgatttaaagtt--tttcttgacat-atcactt-ctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
|| | || | ||| | || || ||||| | | ||| | | | || | | || ||| || || ||||| | || || || || ||||| || || || ||||| || || | || || |||||||| ||||||||||||||||||||
gtaacgctctgcttttcctgcttctggacattttgaactctctttctctttctgggtttgggtttaatgatgattagaattggttgcttgagttcactgcttgccctcacctgtggcatgcctcttcttgcagGAAATCGATTCCATGACGTAGTCGGAAGCGCGTACTACGTGGCTCCAGAAGTTTTGAAGAAAAAATCAGGTCCTGAATCTGATGTGTGGAGTATTGGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaagtttttcttgacatatcacttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
attatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtagcaaagtgatttaaagtttttcttgacatatcacttctttgatctaaccattatgtaacaatgtagGCAAAAAGTTTCATGATATTGTTGGGAGTGCATACTATGTAGCACCTGAAGTGTTAAAACGTAGGTCGGGACCTGAATCAGATGTGTGGAGTATTGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG