Sequence
atgc intronic sequence ATGC exonic sequencegtactgccccttgctttgttcttttgggatttttctacttagattcttttctttctgtgcttaatgagcttactggctctttggtgggcttacagGTGGTTGTGGGTGGAAGAAATAAGTATCTTATCAATGGTCATGTTGCGCAGCCCAGCAGAGTCCAGAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ04936 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ04936 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 1
-----gtactgccccttgc--tttgttcttttgggatttttctacttagattcttttctttctgtgcttaatgagcttactggctctttggtgggcttacagGTGGTTGTGGGTGGAAGAAATAAGTATCTTATCAATGGTCATGTTGCGCAGCCCAGCAGAGTCCAGAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA
| || | || |||| | | | ||| | || || | | | || |||| || ||| || | || || | || ||| | || || ||||| |||| ||||||||||||||||| ||| |||| || || | |||| |||| |||||||||||| || ||||| ||||||||||
aaccgatgctactttccgcattttgatgtctcctaattgatgtaacaag-tgcatctcattct-tgtataacttactaatgtactgttccttacatttgcagATTGTAGTTGGTGGGCGAAACAAGTATCTTATCAATGGCCATCTTGCACAACCTTCCCGAGTGCAGACTCTTTTCCATTCTGTGCAGCTAAATGTGAACA
upper sequence: EFJ04936 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 1
gtactgccccttgctttgttcttttgggatttttctacttagattcttttctttc----tgtgcttaatgagcttactggctctttg-gtgggcttacagGTGGTTGTGGGTGGAAGAAATAAGTATCTTATCAATGGTCATGTTGCGCAGCCCAGCAGAGTCCAGAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA
| | ||| | |||| | | | || ||| | || | | | | | || | |||| ||| | || || | || || ||||||| || |||||| | |||||||| | |||| || || | ||| ||||||||||||||||| || ||||| ||||||||||
------------gtaagtcttatttaaggttttagtgaaaaaaggtttcgtttttaagttttgttaagagtgaattttgtttgtttgtgtgtgtttgaagATTGTAGTTGGTGGAAAGAACAAGTATTTGATCAATGGGAAGCTTGCACAACCAAATCAAGTTCAGAATCTTTTCCATTCGGTGCAGCTTAATGTGAACA
upper sequence: EFJ04936 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S52_57V6.1 (Physcomitrella patens), 3'ss of exon 1
gtactgccccttgctttgttcttttgggatttttctacttagattcttttct--ttctgtgcttaat--gagcttactggctctttgg---tgggcttacagGTGGTTGTGGGTGGAAGAAATAAGTATCTTATCAATGGTCATGTTGCGCAGCCCAGCAGAGTCCAGAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA
| |||| | | ||| | | || | | | |||| | || ||| ||| | || | | | ||| |||| |||||| | || || || || | || ||||| || |||||||| || | || ||||| |||| ||| || ||||||||||||||||||||||||||||||||||
--attgccaacttttcacttcgatgttggcattaccgcatgacttctgccgtggtttagtgtttacttcaagagaatttacgttttaaaattgggtttacagATTGTGGTTGGGGGTCGGAACAAGTACCTCATCAATGGACACCTCGCTCAGCCAAGCAAAGTGCAAAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattcttttctttctgtgcttaatgagcttactggctctttggtgggcttacagGTGGTTGTGGGTGGAAGAAATAAGTATCTTATCAATGGTCATGTTGCGCAGCCCAGCAGAGTCCAGAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA
agcttac putative branch site (score: 3)
ttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgccccttgctttgttcttttgggatttttctacttagattcttttctttctgtgcttaatgagcttactggctctttggtgggcttacagGTGGTTGTGGGTGGAAGAAATAAGTATCTTATCAATGGTCATGTTGCGCAGCCCAGCAGAGTCCAGAATCTTTTCCATTCAGTCCAGCTCAATGTGAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA