Sequence
atgc intronic sequence ATGC exonic sequencegtaatataagtcgatactatcgtgaagtgtttgataagattatattcttttccaacattctcttttttttatgttgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04040.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 13
----------gtaatataagtcgatactatcgtg-aagtgtttgataagattatattcttttccaacattctcttttttttatgt----------tgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
|| |||||| || | | || || |||| || | || |||| | || | | ||| |||| ||||||||||||||||||||| |||||||| || ||||| ||||||||||
tgcacctctggttatataaatcatgaaaagtctgtaaatgttgcatttatgtgaatgctttgtctactgttttgtttacgaatgtgtaatttctttgcagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAACTTGAAG
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 13
--------------------------------------------------------------------------gtaatataagtcgatactatcgtgaagtgtttgataagatt------atattct-tttccaacattctcttttttttatgttgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
| | | || || | | || || | || || |||| | || | | | ||| || |||||||||||||||||| |||||||| || ||||| || |||||||
gtatatattgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttagGTAAATTCAAGCCTGTGATCAAGAAGGCAATGGTGGAGCTTGAAG
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 13
----------gtaatataagtcgatactatcgtgaa-gtgtttgataagattatattcttttccaacattctcttttttttatgt----------tgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
| |||||| || | | || | |||| || | || |||| | | | | | ||| |||| || ||||||||||||||| || ||||||||||| ||||| || |||||||
aaccctggttattatataaatcatgaaaagtctgtacatgttgcatttatgtgaatgctttgtccatagttttgtttacaaatgtgcaatttctttgtagGTAAATTCAAGCCCGTGATCAAGAAAGCAATGGTGGAGCTTGAAG
upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 13
--------------gtaatataagtcgatactatcgtga--agtgtttgataagattatattcttttccaacattctcttttttttatg-----ttgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
| | | | | ||||| | | ||| || | |||||| | | ||| || || |||||||||| ||||||||||| |||||||| || |||||||||||||| |
agcatttatcaggggggttctcatctcagttcatcgtttccattatttagtacatcagctaacctttccatccctttctgaattctaaaactgcttgcagGTAAGTTCAAGCCTGTGATCAAGAAGGCAATGGTTGAACTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtgtttgataagattatattcttttccaacattctcttttttttatgttgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
gtttgat putative branch site (score: 5)
tattcttttccaacat putative PPT
tttgataagattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatataagtcgatactatcgtgaagtgtttgataagattatattcttttccaacattctcttttttttatgttgcagGTAAATTCAAGCCTGTTATCAAGAAAGCTATGGTTGAACTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG