Sequence
atgc intronic sequence ATGC exonic sequencegtaatgattatcagatatggattttgggatagaatgggactcgtgggagactaaatgtatatgttttgcaatgatgtgttgttcagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G02940.1 (Glycine max), 3'ss of exon 3
-----------------gtaatgattatcagatatggattttgggata----gaatgggactcgtgggaga--ctaa-atgt-atatgttttgcaatgatgtgttgttcagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG
| | ||| ||| || || | | | | || | | | ||||| |||| |||| ||||||||| ||| || | ||| | || |||||||||| || |||| | | ||||||| | | | |||||||||||||||||||||||||| ||||||||||| ||||| |||| |||
gtggtatcataatttgactcaagataatctgacattctgtattgatcattctgagttaacatattaggagatgctaacatgttgcatgttttgccatgttgctat---cagCAAGGATGGTGTGATATTCCTGGAACTGTGGATGAAGTTAAAGCAAAGCTACAAATGAGGCAAGAAGGAGCCATCAAGAGGGATAGAGCAATGGCATACT
upper sequence: AT1G72670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G42440.1 (Glycine max), 3'ss of exon 3
gtaatgattatcagatatggattttgggatagaatgggactcgtgggagactaa--atgtatatgttttgcaatgatgtgt-tgttcagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG
| ||||| | || | |||| | | | || || |||| || || |||||| ||| | | | |||| | || |||||||| | || |||| ||| ||||||| | | | ||||||| |||||||||||||||||| ||||||||||| ||||| |||| |||
----gtagtatcata-atttgcctcaagataatgtaacatac-tgagatgctaacaattagcatattttgctatgtttaatattatcagCAAGGATGGTGTGACATTCCTGGAACTATGGATGAAGTTAAAGCAAAGCTACGAATGAGGCAAGAAGGAGCCATCAAGAGGGATAGAGCAATGGCATACT
upper sequence: AT1G72670.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G20430.1 (Glycine max), 3'ss of exon 3
-------------------------gtaatgattatcagatatgg-attttgggatag-aatgggactc---gtgggagactaaatgtatatgttttgca----atgatgtgttgtt--cagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG------
| | || | | || || ||| || || ||| | | | | | |||| | ||| ||| || |||| || ||| | || |||||||| | || ||| | | || | | || ||||||||||||| ||||||||||| |||||||| ||| | | || ||||
gtatcataagtttttcacaatttgcctcaagactgtgtgacataacattctgaaatgttgatgtcatgttaagctagtaaggagatgttaacatttagcataatgtgccatgttattgtcagCAAGGGTGGTGTGACATTCCAAGAACTGCGGAAGAGG------CAAAATTACAAATGAGGCAGGAAGGAGCAATTAAGAGGGATAGAACAAAGGCATATTCTCAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgggactcgtgggagactaaatgtatatgttttgcaatgatgtgttgttcagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG
gactaaa putative branch site (score: 2)
taaatgtatatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgattatcagatatggattttgggatagaatgggactcgtgggagactaaatgtatatgttttgcaatgatgtgttgttcagAAGGGTTGGTGTGATAGCCCGGGAAGTATCAATGAAGTGAGAACGAAGCTACAAATGAGGCAAGAAGGAGCAATCAAGAGGGAGAGAGCTATGGTATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT