Sequence
atgc intronic sequence ATGC exonic sequence...gttgtccattagcgttttatcagtcctacggcaaggaagcttaatccgtcattcctcattgcctcttccatttttttaatgtttttatatgatcttgaagGTGTGGTGCTAGGCAGTCAGGAGATCTAGACTCTTCTAATGAAGAAGCACTTGACGGAATACTTGGATTTGGGAAAGCTAATTCTTCCATGATTTCCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05840.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G29040.1 (Glycine max), 3'ss of exon 3
------gttgtccattagcgttttatcagtcctacggcaaggaagcttaatccgtcattcctcattgcctcttccatttttttaatg--tttttatatgatcttgaagGTGTGGTGCTAGGCAGTCAGGAGATCTAGACTCTTCTAATGAAGAAGCACTTGACGGAATACTTGGATTTGGGAAAGCTAATTCTTCCATGATTTCCCAG
|||| || | ||| || ||| | | | || || | | ||| || |||||| | | ||| |||| ||||| | | | ||| |||||||||||||| || || ||||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || |||||||| ||
attcttattgtgtataataatttaatgttgtctattgaataca---ttgattcat-atttatc----cctcttttaatatttaaatgagtttttttgttgttttgtagGTGTGGTGCTAGACAATCTGGAGATCTAAGTTCTTCAAATGAAGAAGCACTTGATGGAATACTTGGATTTGGAAAAGCTAATTCATCAATGATTTCACAA
upper sequence: AT1G05840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G51920.1 (Glycine max), 3'ss of exon 3
gttgtccattagcgttttatcagtcctacggcaaggaagcttaatccgtcattcctcattgcctc---ttccatttttttaatg-tttttatatgatcttgaagGTGTGGTGCTAGGCAGTCAGGAGATCTAGACTCTTCTAATGAAGAAGCACTTGACGGAATACTTGGATTTGGGAAAGCTAATTCTTCCATGATTTCCCAG
||| || | | |||| || | || | | || | ||| | || | | || || ||| |||| ||||| | | ||| ||||||||||| || || || ||||||||| ||||| |||||||| ||||||| ||||||||||||||||| ||||||||||| || |||||||| ||
gtttcccggtgat-tcttattg--tgtatgataatttaatgttgtctttggttcatatttctccctctttttatatttaaaatgatttttttgctgttttgtaGGTGTGGTGCAAGACAATCTGGAGATCTAAGTTCTTCGAATGAAGAGGCACTTGGTGGAATACTTGGATTTGGAAAAGCTAATTCATCAATGATTTCACA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccgtcattcctcattgcctcttccatttttttaatgtttttatatgatcttgaagGTGTGGTGCTAGGCAGTCAGGAGATCTAGACTCTTCTAATGAAGAAGCACTTGACGGAATACTTGGATTTGGGAAAGCTAATTCTTCCATGATTTCCCAG
ttttaat putative branch site (score: 3)
atttttttaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtccattagcgttttatcagtcctacggcaaggaagcttaatccgtcattcctcattgcctcttccatttttttaatgtttttatatgatcttgaagGTGTGGTGCTAGGCAGTCAGGAGATCTAGACTCTTCTAATGAAGAAGCACTTGACGGAATACTTGGATTTGGGAAAGCTAATTCTTCCATGATTTCCCAG
- - - - - - - - - - - - - - - -caaggaa