Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcttgaatctgctttttctgttatgtagtttctgttttaatacttttgtcttcactcactgtcttcagGTTTGTGAAAGGTCGCTTACTTCTGCAACTGGTGGCCCCACTGGGCCACCTTCTTCAAACTTTGTGAGAGCTGAAATGAAACCAAGCGGGTTTCTCATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34710.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 7
-------------------------------gtgagttcttgaatctgctttttctgttatgtagtttctgttttaatactt--ttgtcttcactcactgtctt-cagGTTTGTGAAAGGTCGCTTACTTCTGCAACTGGTGGCCCCACTGGGCCACCTTCTTCAAACTTTGTGAGAGCTGAAATGAAACCAAGCGGGTTTCTCATCC
| | | | || || || | | ||| | || | | | | | || | | | || ||| ||| ||||||||||||| | |||||| |||||||||||||||| ||||| || |||||||||| ||||||||||||||| || || || | ||| ||
gtactgagcagaatcttgattgttgtgtttttcttgatttaggatgtggcttctttcttaggaagagtttctctcgacacagaatgactatttgtttttgccttgcagATTTGTGAAAGGTCCTTGACTTCTTCAACTGGTGGCCCCACAGGGCCTGCTGCTTCAAACTTCGTGAGAGCTGAAATGCTTCCTAGTGGCTATCTAATTA
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 7
---------------------------gtgagttcttgaatctgctttttctgttatgtagtttctgttttaatacttttgtcttcact-cactgtcttcagGTTTGTGAAAGGTCGCTTACTTCTGCAACTGGTGGCCCCACTGGGCCACCTTCTTCAAACTTTGTGAGAGCTGAAATGAAACCAAGCGGGTTTCTCATCC
| | | | |||| ||| || ||||| ||| | | | | | | | || | ||| | ||||| || || | || || |||||||||||||||| ||||| |||||| ||| |||||| ||||||||||| || || || ||||| |
ttttgatgtgttttttgtcaatgtattgcaaaatatcgaatgattgtttccttttatg--atttaaaactaatttgctcaattgaaattgtgatggttgcagATATGTGAGAGATCATTGACATCCTCAACTGGTGGCCCCACAGGGCCTCCTTCTACAACCTTTGTACGAGCTGAAATGCTTCCCAGTGGTTTTCTAGTTA
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 7
-------------------------------gtgagttcttgaatctgctttttctgttatgtagtttctgttttaatacttttg----tcttcactcactgtctt-cagGTTTGTGAAAGGTCGCTTACTTCTGCAACTGGTGGCCCCACTGGGCCACCTTCTTCAAACTTTGTGAGAGCTGAAATGAAACCAAGCGGGTTTCTCATCC
| | | | || || || | | ||| | || | ||| | | | | | | || | || ||| ||| ||||||| ||||| | |||||| |||||||||||||||| |||||| || |||||||||| | ||||||||||| || || || | ||| ||
gtactgagtggaatcttgattgttgtctttttcttgatttaggatgtggcttctttcttaggaagagtttgtctcgacagaatggctatttttttttttttgccttgcagATTTGTGAGAGGTCCTTGACTTCTTCAACTGGTGGCCCCACAGGGCCAGCTGCTTCAAACTTCATACGAGCTGAAATGCTTCCCAGTGGCTATCTAATTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctgttatgtagtttctgttttaatacttttgtcttcactcactgtcttcagGTTTGTGAAAGGTCGCTTACTTCTGCAACTGGTGGCCCCACTGGGCCACCTTCTTCAAACTTTGTGAGAGCTGAAATGAAACCAAGCGGGTTTCTCATCC
cactcac putative branch site (score: 2)
ctgtcttc CT-rich tract
tgttttaatactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcttgaatctgctttttctgttatgtagtttctgttttaatacttttgtcttcactcactgtcttcagGTTTGTGAAAGGTCGCTTACTTCTGCAACTGGTGGCCCCACTGGGCCACCTTCTTCAAACTTTGTGAGAGCTGAAATGAAACCAAGCGGGTTTCTCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA