Sequence
atgc intronic sequence ATGC exonic sequencegtgccacgaagatcaattaagatctttttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ32911 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ32911 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G001500_T01 (Zea mays), 3'ss of exon 3
----------------------------------------gtgccacgaagatcaattaagatcttt-ttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA
||| | | | || ||| ||| || || | | | | | | |||||||| || || ||||| || ||||||||||||||| ||| | || |||||||| ||||| || ||||| ||||| ||||| || ||| | |||||||
gatcatatggaatgtcaaaatctaactaacttcatactttatgcaattttaagggagatagttctcaactatattgatatattatccttgacttgttcagAGAATAGTAGATTGGCTTGCTAGCAACTTCAAGAAAGATGAACGTATTGATCTTCTGAAGGATAAACAAGCCCTTCAGAGGCTTACTGAGGCAGCAGAGA
upper sequence: EFJ32911 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA16G00410.1 (Glycine max), 3'ss of exon 2
-------------------------------------------gtgccacgaa-gatcaattaagatctttttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA
|| || || ||| | ||||||| || ||||| || | | | ||||||||||||| ||||| || ||||||||||||| ||| ||||| || || ||| | || ||||| ||||| ||||| | || || ||||| || ||||
gtacctttccccttctttcttctcttgtcttgtcttgtctttagtagtgtgagtaatgaatgattttcttttttacttgctaactgcttgtttcctattatagAGAATTGTTGATTGGCTGGCTTCCAACTTCAAGAGAGATGAAGGCATAGACCTTTTGAAAGACAAACAAGCTCTTCAGCGTCTCACTGAGACAGCCGAGA
upper sequence: EFJ32911 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv18s0041g01230.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------gtgccacgaagatcaattaagatctttttattttcttaactctttttcgtcgta-aacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA
| | || | || | || | || || ||| || | || ||||||||||||| |||||||| ||||| |||| ||| ||||| || |||||||| || ||||||||||| ||||| |||| ||||||||||| ||||
gttggaattggttggatgttttttattttttatttttattttttatgatccagttaatttattaatttatttttttgtgaagagatgtcgctgaataatgtttacacttcttgtaaatggaatagAGAATTGTTGATTGGCTAGCACAAAACTTTAAGAGAGATGAAGGTATAGATCTTCTAAAAGACAAGCAAGCTCTTCAGCGGCTCACAGAGACTGCCGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacgaagatcaattaagatctttttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA
tcttaac putative branch site (score: 2)
tctttttattttctta CT-rich tract
atcaattaagatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgccacgaagatcaattaagatctttttattttcttaactctttttcgtcgtaaacagAGAATTGTTGACTGGCTAGCGTCCAACTTCAAGAAAGACGAAGGAATCGATCTTCTCAAGGACAAGCAAGCACTTCAAAGGCTGACAGAGACTGCAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG