Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcatagattgagatcttcttctttcttctttagcctgagtgggagtaactgagattgtttcaaaaccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ19598 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 4
------------gtgagttcatagattgagatctt-----cttctttcttctttagcctgagtgggagtaactgagattgtttcaaaaccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
|| | | || | | | | | | |||||| | || |||| | | ||||||| || |||||||| |||||||| || || ||||||||| ||| ||||| || ||||||||||||||||||||| | ||||| | ||||||||
gtgaacctactaccagttttctgggctgtggctgtgaggtcataacaatccaacggcctgataaaaaaatgctctctttgtct----atcagGTGGCCGCGAGAAGGCACCGGCTGCCTTCTGCAGAAAGGCTCAGACATCCACGGAGAGGTTTGAGATGTGGGGCGATGGTCTCCAGACCAGGTCCTTCAC
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtgagttcatagattga--gatcttcttctttcttcttt-agcctgagtgggagtaactgagattgtttcaaaac-cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
||||| ||| | | || ||||| | | |||| | | | | | ||||| | ||||||| | ||||||||||| ||||| |||||||| ||| | || || |||| ||| |||||||||||||| |||||| |||| || ||||||||||
gtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagttcatagattgagatcttc--ttctttct-----tctttagcc-----tgagtgggagtaac-tgagattgtttcaaaaccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
|| ||| | |||| | | ||| | |||| | | |||| | ||||| ||| | | ||| |||| ||||||| | ||||||||||| ||||| || ||| | ||||||| ||| ||||| ||| ||||||||||||||| ||||| | ||||| || || || ||
gt-agtatacagataaacagtttccgtactttgtgtgaatgattagttgtttactattgggattaatatttgcttggatcaac-ttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCACTGATAGGTTTGAGATGTGGGGAGATGGGCTTCAGACCCGTTCTTTTAC
upper sequence: EFJ19598 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------------------gtgagttcataga--ttgagatcttcttct--ttct---tctttagcctgagtgggagtaactgagattgtttcaaaac--------cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
||| || ||| || | | ||| |||| || | || | ||||| | | | |||| | |||||| ||||||||||||| ||||| ||||| ||||||||||| || |||||||| |||||| |||||||| || ||| | || || || || |||||
gtatgctcttaaaagttatggtgattttctacatgtattcgtgattttgtctcttggtcaccgtcaatggtagggagccaagtgcagagaggtttaagcccgctttaaattctaaatcatatttttggatcttagtaattttg-tcgttttggtatatttgtcgtagGTGGGAGAGAGAAGGCTCCTGCTGCTTTTTGCCGAAAGGCTCTCACTTCCACCGACAAGTTTGAAATGTGGGGAGACGGACTTCAAACTCGTTCTTTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttctttcttctttagcctgagtgggagtaactgagattgtttcaaaaccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
gagtaac putative branch site (score: 2)
ttgtttc putative PPT
tttcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcatagattgagatcttcttctttcttctttagcctgagtgggagtaactgagattgtttcaaaaccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCTCTGACCTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCCTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA