Sequence
atgc intronic sequence ATGC exonic sequencegtgctgctgtgtctttcttttcctcgttttttccgaaagtgcttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ28227 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os11g05480.1 (Oryza sativa), 3'ss of exon 10
-----------------------------gtgctgctgtgtctttcttttcctcgtt-----ttttccgaaagtgcttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
| |||||| | | | || ||| | || | ||||| | || |||| | | | ||| ||||| || ||||| || || ||||| | | || || || ||||| |||||||| ||||| ||||| ||||| |||||||||||||
attcttcaggaagatgaaaccaagctaaaatctgagctcatctttcaagtatacatatacaattctccaatctcactgcatattttt-tatgttgatgcagACATTGACACCCCAGCTGGATCCCCTGACTGAGCAGCAAGTGGTTGGTATCTGCAATCTTCAACAGTCATCGCAACAGGCAGAGGAAGCTCTCTCCCAGG
upper sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os06g15480.2 (Oryza sativa), 3'ss of exon 7
------------------------------------gtgctgctgtgtctttcttttcctcgttttttccgaaagtgcttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
| ||| || || ||| | || || | | | |||| || ||| | ||| || ||||| || || || || |||||||| ||||| || || || || || ||||||||||||||||||||||| || || || ||||
gttttgacacgatcgagtgatcacccacccaattcagcaacaagcaaagaatctgaagctaccattgaccgccattg-ttgatgatgttgtttg----tgcagGTTCTTGCCAGCCATCTTGAGCCGCTGACGGATCAGCAGCTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCGCAGG
upper sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA02G10820.1 (Glycine max), 3'ss of exon 1
------------------------------gtgctgctgtgtctttcttttcctcgt--tttttccgaaagtg-cttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
| | | | ||| | | | ||| | | || || || | | | ||||| | | || ||||| || | ||||| |||||| | ||||| |||||||||||||||||||| || |||||||| ||||||||| | || |
cgagttaggtcaaatccacattctaaaatgatagtaattaacttcacttgtgtacataatttgtttgtttttgactcgtttcttgtattttgggtttcagATCATCAAGAACCACCTTGAGCCATTAACAGATCAGCAGTTGATGGGAATTTGTAATCTACAACAGTCTTCCCAGCAGGCTGAGGATGCTTTAAATCAAG
upper sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv01s0011g03230.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------------------------------------gtgctgctgtg-tctttcttttcctcgttttttccgaaagtgcttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
|||| | | | | ||| | | || | | | | || ||| | | || ||||||||| || |||||||| | ||||| |||||||| ||||| || ||||||||||||||||| || ||||| || |||||||| | || || |
gtaatttgaagatttattgcttttagaccttgaatcttttttatccagttctgcaatggctgaaggaatgtatagtttttttggttgattcacatctatttctattttatttttggagtttcagATACTTGGGAACCAACTTGAACCTTTAACAGATCAGCAGCTGATGGGCATATGTAATCTACAACAGTCCTCACAGCAAGCTGAGGATGCATTATCACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttcttttcctcgttttttccgaaagtgcttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
gcttaac putative branch site (score: 3)
tttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgctgtgtctttcttttcctcgttttttccgaaagtgcttaacgtttttgtgtgacaccacagATACTTATACCTCAGCTTGAACCCCTTACAGAACAGCAGCTCATGGGGATTTGTAATCTACAACAGTCGTCGCAGCAGGCCGAGGATGCTCTCTCCCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG