Sequence
atgc intronic sequence ATGC exonic sequence...ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49810.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 4
ttaatttactctaaaaggtgtaaatgatagaccaggta---ctggaaactttgttaaagtgg--atgctctacctgt--gcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
| | || ||| || | || || | || || | | | | | | | || | || | ||| | | || | ||| || |||||||||||||| || || |||||| | || |||||||| | || ||||||||||| ||||| ||||| || ||| || |||||||||||||||||||
-----taggaccaaggcgtg-aacttctacacttgatagatcttcatattctttaaccccagtaatccactgcttgttatcttagtgcacaccttatt-gcatccagGGTTTTGTTGAGGACCAATTTGGCCTTGGGTTGATTGCTCGGGCTGTTGAAGAAGGGATATCAGTCATAAAGCCTATGGGTATTATGATATTTAACATGG
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G098039_T01 (Zea mays), 3'ss of exon 4
ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaa--ctttgttaaag----tggatgctctacctgtgcctgatgaaatttgtatcc----atattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
|||| | | || | | | | ||| ||||| | ||| | ||| ||| | || || | || |||| || ||||||||||| || || || |||||| | || |||||||| | || || |||||||| ||||||||||| || ||| |||| |||||| |||| |||||||
---------gttaaatgattattcagaccaatcctacattagaatttctttgcttaaggattttgattttct-tttatgtttgccaacatcgatatctttctgcatccagGGTTTTGTCGAGGACCAATTTGGCCTTGGGTTGATTGCTCGTGCGGTGGAAGAAGGGATATCTGTCATAAAGCCTTCAGGTATTATGGTATTCAACATGG
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 4
----ttaatttactcta-aaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
| || | || | | | | || | | | | ||| | | | || |||| | | || | ||||| | ||| |||||||||| || || || |||||||||||||| ||||| || |||||||| || || ||| | || |||||||| | || |||||||| ||||||||||
gggatcttttggcaatatagaaattttttcaattgccttattttctgcctgtttatgaca-tgaatgcagcattctcac---atttattttgtcttt-tatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAACATGG
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 4
---ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgc-ctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
|| | | ||| | | | ||| | | | ||| | || | | || |||| | | | || | | | || |||||||||| || || || |||||||||||||| ||||| || |||||||| || || ||| | || |||||||| | || |||||||| ||||| ||||
cttttggcaaaatagaaatgcttttaat--tgccttattttctgcctattta--tgacatgaatgcagcattctcacatttattttgtcttttgttgcatctagGGTTTTGTGGAGGACCAATTTGGCTTAGGTTTAATTGCTAGGGCAGTTGAGGAGGGGATAGCAGTAATCAAACCAACTGGAATTATGATCTTTAATATGG
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 5
ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgcctgat-----gaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
| |||| ||| | || || || |||| || | | |||| || | || ||| | | || ||| |||||||||| || ||||||||||| || ||| | ||||| ||||||||||| ||||||||| ||||||||||||| || |||||||| || || ||||
---tccaaagggaaaaattgttatccattacaatgggtttgttgcctttcttcttctttttcctctctctctctctctcttttcacaatctttttctctat--agGGTTTTGTCGAGGATCAGTTTGGATTGGGTCTAATTGCTAGAGCAGTTGAGGAAGGAATAGCTGTCATCAAACCAATGGGCATTATGATCTTCAATATGG
upper sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S76_18V6.1 (Physcomitrella patens), 3'ss of exon 4
ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaactttgttaa--agtggatgctctacctgtgcctgatgaa-atttgtatccatatt--cagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
|| || || | | | | | || || || || ||||| || | | | | || | |||| | || ||||| |||||||| ||||||||||| ||||||||| |||| || || || || || || || |||| | ||| | || | | ||||| || || |
-----ttctgctgtaatcaactacttcttgcaaggtcgatgaaattggcgtaaaggagtggccgcattgctgtatcataatttatgtttgggttgtcgttggcagGGATTTGTTGAGGATCAGTTTGGGTTAGGTTTGGTTGCAAGGGCTACAGAGGAGGGTATTTCAATCATTAGACCGACTGGAAAGCTCATATTCAATATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgttaaagtggatgctctacctgtgcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
gcctgat putative branch site (score: 4)
aaatttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaatttactctaaaaggtgtaaatgatagaccaggtactggaaactttgttaaagtggatgctctacctgtgcctgatgaaatttgtatccatattcagGGTTTTGTTGAAGATCAGTTTGGCTTAGGTTTGATTGCCAGAGCAGTTGAAGAAGGAATATCTGTCATCAAACCTGCAGGGATTATGATATTTAACATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - ctctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa