Sequence
atgc intronic sequence ATGC exonic sequence...agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16190.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 3'ss of exon 1
agtttttttttttccgatgaaatggatgggttgagtg-agtgtatttgtctatgagttcttacatggttatatcctggaatttttctactt---tgctttgaa---gATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
||| ||| | || | | | | | | || | || || || | | || || | | | |||||||| || || || | ||| ||||| || ||||||| |||||||| |||| | || || | ||| || || || || || || |||||||||||||| ||||||||||||||||
----tttatttcttgtctgctacgtcttctataattatagcaaaaatggctctgc-tacatatataaccgt--tccaggatttttctgtttgtacactatggaacagATTATGGCTGTCAAGAAGATCATTGAAGAGATACAAGGAAAGGATAGCTACCCATGGGGCCAACAGTTGCTGATTCACAATGGCAAGGTTTTGAAAGATG
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 1
----agtttttttttttccgatgaaatggatg-ggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
| || | | | | || | ||||| ||||| | ||| | | | | || | | || | || || || | |||| ||||| |||||||||||||| ||||| |||| | ||||||| |||||| || || || ||| | |||||| |||||||||||| ||||||||||
ataatgcttgtcagctaactgttttgtgatcgtagttgaatgagttttattggcattcaatattttgtcaaggttctactaaaggttccttatttacc-----agATTATGGCTGTGAAGAAGAATATAGAAGAGATACAAGGGAAAGACAGCTATCCATGGGGCCAACAACTGCTGATTTTCAATGGAAAGGTCTTGAAAGATG
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G44910.1 (Glycine max), 3'ss of exon 1
--------agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
| | | || || | ||| | | | | | | ||| || | || || || | || || ||| ||| | | |||| ||||| || ||||||||||| |||||| |||| |||||||||| || || ||||| |||||||| || ||||||||||| ||||||||||||||||
gtcagtcatatgatctcattcccaacccaat---tctgctttttaatttcattcttccaaa---tcctatgcatttcttaattgtgatgttttatcttcacctc--agATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATGGTAAGGTTTTGAAAGATG
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G00490.1 (Glycine max), 3'ss of exon 1
--agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctg-gaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
| |||| | | ||| || | | | ||| | || | || |||| ||| | || |||| || | || | ||||| || |||||||||||||||||| |||| | ||||| || || || ||||| |||||||| |||||||||||||| ||||||||||||||||
ggaaaattttgaagtgctatgtttcaaattctattgtttatcagccgaaattatcaatttgt---tgtttattagctgagtgttcttctttttgtcacctcagGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGCTGATTCACAATGGTAAGGTTTTGAAAGATG
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G23930.2 (Glycine max), 3'ss of exon 1
-agttttt---ttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagtt-cttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
| |||| | | | |||||| || | || | || | ||||| || ||| ||| | | | | | |||| | || | ||||| || |||||||||||||||||| |||| | ||||| || || || ||||| |||||||| ||||||||||||| ||||||||||||||||
taattttgaagtgctattttttgaaatctattgttt-atcagctgaaattgtcaatttgttgtttaattagctgaagttttctgcttttttgtcccatc----agGTTATGGCTGTCAAGAAGAATATTGAAGATGTACAAGGAAAAGATAATTACCCATGTGGACAGCAATTGTTGATTCACAATGGCAAGGTTTTGAAAGATG
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G44910.2 (Glycine max), 3'ss of exon 1
--------agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
| | | || || | ||| | | | | | | ||| || | || || || | || || ||| ||| | | |||| ||||| || ||||||||||| |||||| |||| |||||||||| || || ||||| |||||||| || ||||||||||
gtcagtcatatgatctcattcccaacccaat---tctgctttttaatttcattcttccaaa---tcctatgcatttcttaattgtgatgttttatcttcacctc--agATTATGGCAGTCAAGAAGAATATCGAAGATGTACAAGGCAAAGACAATTACCCATGTGGACAGCAATTGCTCATTCACAATG------------------
upper sequence: AT1G16190.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0018g01400.t01 (Vitis vinifera), 3'ss of exon 1
-----agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
| | | | |||| ||||||| || ||| ||||||| || | | | || | | | | ||| | || || ||| || |||| | |||||||| ||||| || ||||||||| |||| | |||||||||||||| |||||||| |||||| ||||||| ||||||||||| ||||||||||
actctgttcatctgtgttcccatgaaatatat---ttgcctgagtgtgtt-gcaaacaccacatgacttaatgaaaaccttggtaattgcttgtttaatt-gaagGTTATGGCGGTAAAGAAAAACATTGAAGATGTACAAGGAAAAGACAACTATCCGTGTGGGCAACAATTATTGATTCATAATGGAAAGGTCTTGAAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
ttcttac putative branch site (score: 2)
tttttctactttgctt putative PPT
aatttttctacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtttttttttttccgatgaaatggatgggttgagtgagtgtatttgtctatgagttcttacatggttatatcctggaatttttctactttgctttgaagATAATGGCGGTGAAGAAGAATATTGAAGATTCACAAAGCAAAGACAACTATCCTTGTGGGCAGCAATTACTGATTCACAATGGAAAGGTTTTGAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - -gatgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttacat