Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctgatttattcattggaacagtagcctagctccttacggtgcaccattatctcactgaaataagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02560.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
--------gtaagttctgatttattcattggaacagtagcctagctcctta--cggtgcaccattatctcactgaaataagtctt---tctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
| | | ||| | || |||| | | | | || | | ||| | | ||||| || || | ||| ||| ||||| |||||||| |||||||||||||| ||||| ||||||||||| |||| || | || || ||| || | | | || || || ||| ||||
aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 8
gtaagtt-ctgatttattcattggaacagtagcctagctccttacggtgcaccattatctcactgaaataagtctt---tctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
||| || |||| | | | || || |||| || || ||| | | ||||| || || | ||| ||| ||||| |||||||| |||||||||||||| ||||| ||||||||||| |||| || | || || ||| || | | | | || || || ||| ||||
gtacgtaattgatgctcttacagtaatagataaatagcatct----gt------ttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATCTGCAATTATAGTATCTCGTCCTGAA
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 8
gtaagtt-ctgatttattcattggaacagtagcctagctccttacggtgcaccattatctcactgaaataagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
||| || || | | | | | | | | | ||| | | || || | | | | ||| | ||| | ||| ||||||||||||||||||||||||||||| ||||| ||||||||||| | || ||| | || || |||||| | | | | || || || ||| ||||
gtacgtcactattatgctgacagcgattccatacagattaatta-gctccagt-ttgtgtaattaaaacttttaacattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCAGCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G053644_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------gtaagttctgatttattcattggaacagtagcctagctccttacggtgcaccatt-atctcactgaaa-taagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
| || | | || | | | ||| | ||| || | || | | | | ||| | | ||| | ||| ||||||||||||||||||||||||||||| ||||| ||||||||||| | || ||| | | || |||||| | | | | || || || ||| ||||
gtatgttcccctatttttgcgacttatggtgatgtcccttgctgtctcggcaataaagtatcaccagactgcaggatttaggccgcccaggtccaattgtattgtaataaaaacttttaaactggtcagtttgtgtaattaaaactttttaacattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCATCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
----gtaagttctgatttattca-ttggaacagtagcctagc-tccttacggtgcaccattatctcactgaaataagtct-ttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
|| || || || | | | || | | | || | | | | | | | | | || | | | ||| | ||| || ||||||||||| || |||||||||||||||| ||||||||||||| |||||||||| || |||||| |||||| ||| || ||||| ||| |||||
gtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 8
----gtaagttctgatttattcattggaacagtagcctagctcctt-acggtgcacc-attatctcactgaaataagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
|| || || || | | | | | | || || || | | | | ||| || |||| | | ||| ||| |||||||||||||| || |||||||||||||||| |||||||||||| |||||||||| || ||||| |||||| ||| || ||||| ||| |||||
gtatgtcctttttggttcccttagctgcagtatggattaattctttcatgatattcttgttaatcatctcaaatgtgctgtatttt---gcagTGAGAGTGCAAATGAATATACAGATGATGAAGATGTAAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGTTTAGCAGCATTGATTGTTTCTCGTCCTGAG
upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtt-----ctgatttattcat--tggaacagtagcctagctccttacggtgcaccattatc-tcactgaaataa-------gtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
||| ||| ||| ||||| || | || | | | || | || | | || | ||| | || | || | | | | || |||||||||| ||| || ||||||||||| |||| ||||||||||||| | |||||||| || |||||| |||||| || || ||||| || ||||
gtatgttgttcactggtttatgtatatttgagctatcgtgtaaataatttatgcatgcttgaattgttactaatatcacagtactgtatcttgtatttgtagTGAGAGTGCAACTGAATATACAGATGATGAGGATGTCAGCTGGAAAGTTCGAAGAGCAGCAGCTAAATGCTTAGCAGCTTTGATTGTTTCTCGACCTGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagctccttacggtgcaccattatctcactgaaataagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
tctttctttctcac CT-rich tract
tgaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctgatttattcattggaacagtagcctagctccttacggtgcaccattatctcactgaaataagtctttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG