Sequence
atgc intronic sequence ATGC exonic sequencegtagcgtttcttcttttccttttcttttttttttcttgattgttctttgtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ18574 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ18574 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA08G43290.1 (Glycine max), 3'ss of exon 2
------------------------------------gtagcgtttcttcttttccttttcttttttt--ttt--cttgattgttcttt----gtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG------------------------------------
||| ||| ||||| | | | | |||||| ||| ||||| | | ||| | ||||||||||||| || || || || || |||||||||||||||||||| ||||| | | |||||
gtttgtgttttctacatctattcatgaatttcccttgtattctttattcttataatctacattttttggtttgacttgaatttctttttgttgcagTTGGAAATGGAGGACGGGGACGAGATTGATGCCATGCTTCACCAGACAGGAGG--TTCTGTTGTCTGAAGGATGTGATTACTTTGCTCCTCATTATAAGTAG
upper sequence: EFJ18574 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------gtagcgtttcttcttttccttttcttttttttttcttgattgttc---tttgtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG------------------------------------
| ||||| | | | | ||| || | || | ||| ||| || | |||||||||||||| ||||| || ||||| |||||||| |||||||| || || | | |
gtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGTGG--TGGTGCTAAAAATGGCCTGAAGCTCTTCTGCTTTTAGTGGCGGTTAT
upper sequence: EFJ18574 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------gtagcgtttcttcttttccttttcttttttttttc---ttgattgttctttg---------tagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGT---TGTAG-------------------------------
| | | | |||| ||| | | | | | | | |||| ||| | |||||||| ||||| |||||||||||||| ||||| ||||| |||||||| | | | |||||
ttttcttataaacaagtgatctgaatcccacattgggcatccctcacatatttcttttggtgtctcatgtgaaatgggcaacattttgatatgggtttagCTTGAAATGGAGGATGGTGATGAAATAGATGCAATGCTGCACCAAACTGGAGGGGTTGCATGGATGTAGATATATAATATATGGGAAAAGCATGGCAAGG
upper sequence: EFJ18574 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S317_15V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------------------------------------------gtagcgtttcttcttttccttttcttttttttttcttgattgttctttgt---------agTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG----------------------------------
|| || ||| |||| | |||| || | ||| || || | |||||||||||||| ||||| || |||||||||||||| || ||||| |||| | | |
gtatgcatttcaagttactgtatatttatcttgttctcagtagtagaattttagcatcccgtggctttgtttttctgtcgagatggacggttcacttgattcaactttctcgatttactcacttacctgtctaattttgtttccaaatgttttgtgttttaacataagaattttccacgttgatgtgacagCTTGAAATGGAAGATGGAGATGAGATCGATGCCATGCTTCATCAAACTGGTGGAAATGCTTGCTGACTTGAATGCCGATGCAGGAGTTCGAACATCGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagcgtttcttcttttccttttcttttttttttcttgattgttctttgtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG
tcttgat putative branch site (score: 4)
tttcttcttttccttt CT-rich tract
ttttcttttttttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcgtttcttcttttccttttcttttttttttcttgattgttctttgtagTTGGAAATGGAAGATGGCGATGAAATAGATGCCATGCTTCACCAGACTGGAGGAATGCCGTTGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA