Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcaatgtgaaaaagtgattgttttgtcctttgttgttgttgaggatagtatattgtgctttgttatttaaccatggatgctaaattcctttagGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 2
gtatgtcaatgtgaaaaagtgattgttttgtcctttgttgttgttgaggatagtatattgtgctttgttat-ttaacc--atggatgctaaattcctt--------tagGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
| | | || | | ||| |||| | || | | | || ||||| || | ||||| | | || | ||| | |||||| | | ||| | | |||||||||||||||||| || ||| |||||||| ||||| ||||| ||||| ||||| |||||||| || || || |
-------acttttgtaatgcatctagttta--cttttgtaaagtgggtactggcttactgtgcattacttcactaacctcacagctgacatatttttgggtaaccatagGGACGGAAGGAGGATAAAAAAATGGAGGAAGATGATAGGTGTTGGTGGTAGTGACTGGAAACATTATGTTAGAAGAAACCCTCATGTGGTTAAAAGAAGA
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G047223_T03 (Zea mays), 3'ss of exon 2
gtatgtcaatgtgaaaaagtgattgttttgtc---ctttgttgttgttgaggatagtatattgtgct----ttgttatttaaccatggatgctaaattcctttagGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
||| || ||| ||||| || | || | || | ||| || | | | ||||| | | | || || || ||||||||| | || | | |||||||||||||||||| || ||| |||| ||| ||||||||||| ||||| || || |||||||| || || |||||
----acttgtgtaaatcagttattgtcttacttcaccttcctatttctctaaataaactaccttacaagtgcttttattctatt-tcttttttatgttgctatagGGAGGAAAGAAGGATAAGAAAATGGAGGAAGATGATAGGTGTTGGTGGTAATGACTGGAAGCATTATGTTAGAAGGAACCCTCATGTGGTTAAAAGGCGA
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 1
--------gtatgtcaa-tgtgaaaaagtgattgttttgtcctttgttgttgttgaggatagtatattgtgctttgttatttaaccatggatgctaaattccttt----------agGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
|| | ||| ||| | ||| || | | || | |||| ||| || | | || || |||| ||| | | | | ||| | |||||||||| || || | ||||||||||||||||||||| ||| || ||||| ||||||||||| | |||||||||||||||||||| ||
gtatttttgtttttcacctgttgatttgtgtttttctgtgttttaagcatgaatgagtata-taaaatatggccagtgattttacctgtattaccatttacctctcatcagATATAGGGAGGAGAGAAGGGTTAGAAAATGGAGGAAGATGATTGGGGTTGGTGGCAGTGACTGGAAGCATTATTTAAGGAGAAAACCTCATGTTGTTAAA------
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 2
gtatgtcaatgtgaaaaagtgattgttttgtcctttgttgt-tgttgaggat-----agtata----ttgtgctttgttatttaaccatggatgctaaattccttt----------agGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
| | ||| | | |||| ||||| ||| ||| | || || || |||||| |||| | ||| ||| | | | | ||| | |||||||||| || || | ||||||||||||||||||||| ||| || ||||| ||||||||||| | |||||||||||||||||||| ||
--gtatttttgttttacacctattgatttgtgtttttctgtgttttaagcatgagtgagtataaaaaatgtggccattggttttacctgtatttccatttacctctcattagATATAGGGAGGAGAGAAGGGTTAGAAAATGGAGGAAGATGATTGGGGTTGGTGGCAGTGACTGGAAGCATTATCTAAGGAGAAAACCTCATGTTGTGAAA------
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtcaatgtgaaaaagtgattgttttgtcctttgttgttgttgaggatagtatat-tgtgctttgttatttaaccatggatgctaaattccttt---agGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
| | ||| || | | | | | ||| | |||| || | |||| | | ||||| || | ||| |||||| |||||||| | | || | |||||||||||| |||||||||| ||| || |||||||||||||||||||||||||| |||||| |||| || || || ||
-ttttgcaaaatggagtttttttggctgtgtttgtgtatgtttttctct-tgctataagcattaccggatattttactacaagacataaggtcctttttcagGGAGGAAAGACGGGTTAGAAAATGGAGGAAAATGATTGGAATTGGAGGGAGTGATTGGAAGCATTACGTTAGGAGGAAACCTAATGTGGTTAAAAGACGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaggatagtatattgtgctttgttatttaaccatggatgctaaattcctttagGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
tgctaaa putative branch site (score: 2)
ttccttt CT-rich tract
tttgttatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcaatgtgaaaaagtgattgttttgtcctttgttgttgttgaggatagtatattgtgctttgttatttaaccatggatgctaaattcctttagGGAGGAGAAGAGAGTGACAAAATGGAGGAAGATGATTGGAACTGGGGGTAGTGATTGGAAGCATTACGTTAGGAGAAAACCTCATGTTGTCAAGAGGCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG