Sequence
atgc intronic sequence ATGC exonic sequencegtaattccattcttactcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48600.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os05g47545.1 (Oryza sativa), 3'ss of exon 7
gtaattccattcttactcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
|| | | | | | || || || | | | || | || | | ||| || | |||||| || || || |||||||||| ||| |||| |||||||| ||||||||||| || |||||||| || || || || || || |||||||| ||||||||
gtcagttgaaca--atttccttgcctctattaaaatgtcaacatttac------------tcattcaaacatgcttattga--tgaacagAAACCACAAAGGAATTTGTGGATAAGCTGGATCTTAAACCTGGACAGAAAGTGCTTGATGTTGGGTGCGGAATTGGAGGCGGCGACTTCTATATGGCTGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G060886_T01 (Zea mays), 3'ss of exon 7
gtaattccattcttactcttttatcttcatatg-gacatacgtacttgtattgtctgagtgt-tatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
|| | | | | | || || || | || || | | || ||| ||||| | | | | |||||| | | ||| ||||||||| || ||||||||||||| ||| |||| || ||||| ||||| || || || |||||||| ||||| || || ||||||||||| || ||||| ||
gtgagtgcggcaatccctgttaattttaacttgtgatgttc-tatttgcattgtgtccttaaatgttgttatgta-tcactgtcc--aacagAGACTACAAAAGAATTTGTGGACAAGCTGGATCTCAAACCTGGACATAAGGTGCTTGATGTTGGATGTGGAATTGGGGGAGGTGACTTTTATATGGCCGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G122296_T01 (Zea mays), 3'ss of exon 7
gtaattccattcttactcttttatcttcatatggacata-cgtacttgtattgtc--tgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
|| | | | | | |||| || | | | | ||| |||| || | || | | | |||||| || | | | || |||||| || ||||||||||||| ||| || | ||||| || || ||||| || || |||||||| ||||| || || ||||||||||| || ||||||||
gtgagaggacacatccctttttgtcatttttttgtgatatcgtatgtgcagtgccattaaatgttattatt-catcactatgcacc-----agAGACTACAAAAGAATTTGTGGAGAAACTGAATCTTAAGCCTGGGCAGAAGGTGCTTGATGTTGGATGTGGAATTGGGGGAGGTGACTTTTATATGGCTGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G33790.2 (Glycine max), 3'ss of exon 6
---gtaattccattcttactcttttatcttca----tatggacatac-gtacttgtattgtctgagtgttatcttt-atgttct--tgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
| | | || | |||| | || | || ||| ||| |||| |||| || | | | |||| ||||||| | || | | |||| || || || || |||||||| ||| ||| || || || || |||||||| || ||||||||||||||| | || |||||||| ||||||||||||||
tctattgtcctggtcagaatcttgaagattaggtgctgtgtgtttacagtagttgt-ttgtgtgtttctaacctttgatgttctgctcattgcttgggcagAAACGACAAAGGAGTTTGTGGCAAAGCTGGGACTAAAGCCTGGTCAGAAAGTTCTGGATGTTGGTTGTGGTGTTGGGGGAGGTGATTTCTACATGGCTGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G11580.1 (Glycine max), 3'ss of exon 6
---gtaattccattcttac-----tcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgtt--ttcctta-acagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
||||| | ||| | ||| | | | |||| || || | ||| | ||||| || || | |||||| ||||| ||||| || ||||| ||||| ||| ||| || ||||| || |||||||| || |||||||||||||||| || ||||||||| | |||||||| ||
gtgctaattaaaatctagaaggtgccatttgtttatttttgga-atcagtcatagtagatttcatgtgtttctaaagtgcaagtgctcattccttgtacagAAACAACCAAGGAATTCGTGGCAAAGTTGGGACTAAAACCTGGCCAGAAAGTACTGGATGTTGGTTGTGGTACTGGGGGAGGTGACATTTACATGGCAGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G30650.3 (Glycine max), 3'ss of exon 3
-----------gtaattccattct-tactcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
||| | ||| | || | | || | | | |||| | ||| | || | | | | | || ||| | | |||| ||||| || ||||||||||| ||| ||| | ||||| || || ||||| || |||||||||||||||| || ||||||||| | |||||||||||
tttaaatatatttaagcctattttgtaatatattttttggaatcaatcatat-tgtagatatcttatgtttctgaagtgcaagtgcttaatgcatgtg-cagAAACAACAAAGGAATTTGTGGCAAAGTTGGGATTAAAACCTGGCCAAAAAGTACTGGATGTTGGTTGTGGTACAGGAGGAGGTGACATTTACATGGCTGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 6
--------gtaattccattcttactcttttatc--ttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
| | |||||| | |||| || | | ||| | || | | | | | || | | | | | |||| ||||| || ||||||||||| ||| |||| ||||| || || ||||||||||| || || |||||||| || || |||||||||||||||||||||||
ctaagcacaaattgccattcatgagaaattattcgtttaattaactataataaattccaattaccaattcttgcactgagaaaatcccgaatttgatcagAAACAACAAAGGAATTTGTGGCTAAGTTGGAGCTTAAGCCCGGCCAGAAAGTCCTGGACGTAGGTTGTGGCATTGGCGGAGGTGACTTCTACATGGCTGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g05200.t01 (Vitis vinifera), 3'ss of exon 7
gtaattccattcttact---cttttatcttcat--atggacatacgtacttgta-ttgt--ctgagtgttatctttatgt-tcttgttttcctt-aacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
| || || || || ||| |||| || || | | | || || || | | || | | | | ||| ||| || |||||| ||||| |||||||||||| | || |||||||||| || | || || ||||||||||| || ||||| |||||||||||||||||||||||||| ||
ccagtttcagtcaaacaaaattttcgcaatcattggaggttattcacattcttaactgcaactaatttaaatttctctttaccttatttgatttgaacagAAACAACAAAAGAATTTGTGACAAAATTGGACCTTAAGCCTAGCCAAAAGGTCCTAGATGTAGGCTGTGGCATCGGTGGAGGTGACTTCTACATGGCAGA
upper sequence: AT1G48600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g02430.t01 (Vitis vinifera), 3'ss of exon 7
------gtaatt--ccattcttactcttttatcttca---tatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
| ||| | | || | | || | | | ||| | | | ||||| | | | || | | || | | | | |||||||||| ||||||||||||| || ||||||||||||| || ||||| ||||||||||| || ||||| || || |||||||||||||| ||||| ||
cagataattattagctggttttcatgaatcatttgaaattcagtgacttgttaattagtattcttctaat-ttctttgagtgaaccctggtctttgagcagAGACAACAAAAGAATTTGTGGGAAAACTGGACCTTAAACCTGGCCAGAAGGTCCTAGATGTGGGCTGTGGCATTGGAGGAGGTGACTTCTATATGGCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
tctttatgttcttgtt CT-rich tract
ttatctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccattcttactcttttatcttcatatggacatacgtacttgtattgtctgagtgttatctttatgttcttgttttccttaacagAGACAACTAAAGAATTTGTGGCGAAGATGGACCTTAAACCGGGACAGAAAGTCCTAGATGTTGGTTGTGGTATCGGTGGAGGTGACTTCTACATGGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG