Sequence
atgc intronic sequence ATGC exonic sequence...gtttgtccatgtgaaaattgacaactgaagatgtaaatacttgagtggtgtttttcaccttgcttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51710.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 9
---gtttgtccatgtgaaaattgacaactgaagatgtaaatacttgagtggtgtttttcaccttgcttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
|| | | | || | | || | ||| ||| | | || | | | | || || ||| |||| | | | || ||| | |||||| ||||||||| ||||| || | ||||| |||||| || |||||| | || ||||||||||| ||||| || |||||| | |||||||||
actagttacctgtattgaattaaaaaaaactatttgttcataa--gcacgatgacaatgctccagtgtgcttctatttattaatgttggcttctat-ttgcagGGTCCATTGTGCAGAAAGTGGTGAAGAGAGTTTAGAGAGAGAATCAGTTTATTCTTTGAAGTGTCATATATCTCATGATGTAAACCACCTTCATGAAGGA
upper sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G017086_T02 (Zea mays), 3'ss of exon 9
gtttgtccatgtgaaaattgacaactgaag-atgtaaatacttgagtggtgtttttcaccttgc-ttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
| | | | | |||| | | | | ||| || | | | || || || | || | || || ||| | | | | | ||| | || ||| ||||||||| || || ||| ||||||||||| |||||||| || || ||||||||||| || || |||||||| | ||||| |||
tcataacaactggtagattgggtgttcatgtaagtatgtaacaaatatgaaatgatcgccgtgaacttgtgatatttgtt--gatgaatgctttttttccagGGTCCACTGTGCAGAAAGTGGTGAGGAGAGCATGGAGACAGAATCAGTATATTCCCTTAAGTGTCATATATCTCAAGATGTGAACCATCTTCATGAGGGA
upper sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 9
gtttgtccatgtgaaaattgacaac--tgaag---atgtaaatacttgagtggtgtttttcaccttg---cttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
| | || ||| ||| ||||| || |||| || | || || | | ||| | | ||||| || | | ||| | |||| | ||||||||||| ||| |||||||||||||| ||||| ||||| ||||| || ||||| || |||||||| || |||||||| ||||| |||||
------aaaagagacaatccacacttttgaagtttattaaaatgctc-attgatgcccatgaaattgtatcctgtttaatgtagt-cattttgataacaacttgttagGATTCATTGTCAAGAGAGTAATGAAGAAAGCTCAGAAACAGAGTCTGTTTATTCACTTAAATGCCACATATCACAGGAGGTGAACCATTTGCACGAAGGG
upper sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 9
gtttgtccatgtgaaaattgacaac---tgaag---atgtaaatacttgagtggtgtttttcaccttg---cttagttaatttaattcggattggttcatgtgctgt-agGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
| | || ||| ||| ||||| || |||| ||| | || ||| | | ||| | ||||| || | || | | || ||| ||| | ||||||||||| ||| |||||||||||||| |||| ||||| ||||| || ||||| || ||||| || || |||||||| |||||||||||
-------aaagagagaatccacactttttgaagtttattaaaatgctt-actgatgtccataaaattgtatcccgtttaatgtagtc--attttgataataacttgttagGATTCATTGTCAAGAGAGTAAGGAAGAAAGCTCAGAAGCAGAGTCTGTTTATTCACTTAAATGCCACATATCGCAGGAGGTGAACCATTTGCATGAAGGG
upper sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 9
-gtttgtccatgtgaaaattgacaactgaagatgtaaatacttgagtggtgttttt-caccttgcttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
||| | | || | | | || || |||| | || | || ||||| | || ||| || ||| | | | |||| ||||||| |||||||||| ||||| ||||||||||| ||||| || ||||| || ||||| || |||||||| || |||||||| ||||||||||||
tgttgggttgtctgttcttctattttgacatatcctaaaggatgagagtctcttatacattatgcttttctggtt--attttcttttgttggttttgtttagGATGCATTGCGAAGAAAGTGGTGAAGAGAGCTCAGAGACTGAATCAGTTTATTCACTTAAATGCCACATATCACACGAGGTGAACCATTTGCATGAAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtttttcaccttgcttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
atttaat putative branch site (score: 4)
ttagttaatttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtccatgtgaaaattgacaactgaagatgtaaatacttgagtggtgtttttcaccttgcttagttaatttaattcggattggttcatgtgctgtagGTTGCATTGTCAAGAAAGTGGCGAAGAAAGCTCAGAGACAGAATCTGTATATTCTCTAAAATGTCATATATCACATGAAGTGAACCACTTGCATGAAGGA
- - - - - - - - - - - aactgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggattgg