Sequence
atgc intronic sequence ATGC exonic sequencegtaagggcgatatcaaatgtggtttattttgaatatttgggatcaaatgattgctgttgtgatttaactttatgtttttggttcttctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
--------------------------gtaagggcgatatcaaatgtggtttattt----------tgaatatttgggatcaaatgattgctgttgtgatttaactttatgtttttggttcttctt------tttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
|| | ||| | | | | | | | | || | | || ||| || | | || | |||| | ||| || | |||| |||| ||||| |||||||| ||| || ||||| || ||||| | ||||| || || || |||||||| |||||||| || |||||||| |||||||||||
gtaagattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgttttgtactctgttataacagggttaacttgaacctgtgtgtgatattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
----------------------gtaagggcgatatcaaatgtggtttattt-tgaatatttgggatcaaatgatt-----gctgttgtgat----ttaactttatgtttttggttcttctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
| | ||| || | | |||| | | | | || | ||| || ||||| | | |||||||| | || | | | |||| |||| ||||| |||||||| ||| || ||||| || ||||| | ||||| || || || |||||||| |||||||| || |||||||| |||||||||||
gtaagattgatctttacatctcattattaggatctc---cgcgccttatctgtatacaattagcgctccatgttttgtactctgttataacagggttaactttgaacctatg--tgtgatattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 4
------------gtaagggcgatatcaaatgtg-gtttattttgaat---atttgggatcaaatgattgctgttgtgattt---aactttatgtttttggttctt--ctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
||| ||| ||| || || || |||| | | | || ||| | || || || | || | || | ||| ||||||||||||| |||||||||||| ||||||||||| ||||||||||| || || ||||||||||||||||||| || |||||||| || ||||| || ||
gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
gtaag-ggcgatatcaaatgtggtttattt--tgaatatttg------------ggatcaaa------tgattgctgttgtgatttaac-tttatgtttttggttctt---ctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
||||| || |||| || | |||||| || ||| ||| | |||| | || ||| | |||| ||| | || ||| | || ||||||||||||| |||||||||||| ||||||||||| ||||||||||| || || ||||||||||||| ||||| || |||||||| || ||||| || ||
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatttgttaattcagttttctgatttcctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 4
----gtaagggcgatatcaaatgtggtttattttgaatatttgggatcaaatgattgctgttgtgattta-actttatgtttttggtt-cttctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
| || | || | ||||| ||| || | | || | ||| ||| | | || | ||| | | | | || || || ||| || | ||||||| | ||||| || || || | |||||||| | || || || || || | ||||| |||||||| |||||||||||||| |||||||| ||
tctaatcagtg-aatgtgaaatggagtta--ttgaactcttagtcatcttttgaacggtagggtaacttacagtgtgttttatttgtggcttgattcatgcagACCTCATCAATGTATTCGAAGTCTTCTTGCCTCAGCTCTTACTCTACCCTAATCCTACCGATCCTTTGAATGGTGAAGCTGCTGCGTTGATGATGCGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaatgattgctgttgtgatttaactttatgtttttggttcttctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
atttaac putative branch site (score: 3)
ctttatgtttttggtt CT-rich tract
atttaactttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggcgatatcaaatgtggtttattttgaatatttgggatcaaatgattgctgttgtgatttaactttatgtttttggttcttctttttttcagACCTTGTGAATGTGTTTGAGACATTTCTTCCTCAGCTTCTTCTGTATCCAAACCCATCAGATCCATTGAATGGAGAAGCTGCTGCGTTAATGATGCGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC