Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ17606 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
------------------------------gtttgtttgtgttcttttttttctcttgtt-tttatgacttgtctctct---ctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
| | | ||| | | | | ||| |||||| || | || ||| | || || |||||||||||||| || |||||| | ||||||||||| ||||| || ||||| || ||||| || || || |||
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatttgctgtaatttatgttttagtttgctaattcctcctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 2
------------------------------gtttgtttgtgttcttttttttctcttgtt-tttatgacttgtctctct---ctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
| | || | | ||| | |||| || | || ||||| || | |||||||||||||| || |||||| | ||||||||||| ||||| || ||||| || ||||| || || || |||
tgcacactgaggttatagcatctctatctactccatccgttccaaaatataagcactgtaatatatgttttagtttgctaactcctcttttcacaaacagCGTTTTGCTGCAGTTATCATGAGAATAAGAGAACCGAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG
upper sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 2
----------------------------------gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctct-ctctcttctct-tatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
|| || | | || | ||||||| ||| |||| |||| | | |||| || ||| || |||||||||||||| || |||||| | ||||||||||||||||||||||| || || ||||| || || || |||
cattctttctttgttatgattatataatgtagcaacctgatttt-tgctgtgttttctca-gttattatattttgtatgttgactcttttatctgtaaacagCGTTTTGCTGCAGTAATCATGAGAATAAGAGAACCCAAAACCACGGCACTGATATTTGCATCGGGTAAAATG
upper sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 3
----------------------------------gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctct-tatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
| | |||| || | |||| ||||| || |||| || | | || || ||| || |||||||||||||| || |||||| | |||||||||||||||||||| || || || ||||| || || || |||
tctcagttatgatgataatgatataatgtcacatgctggtttttgctaagttttctctct-attattatatttttatcttgacccttttatctgtaaacagCGTTTTGCTGCAGTCATCATGAGAATAAGAGAACCCAAAACCACAGCACTGATATTTGCATCGGGTAAAATG
upper sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA03G04500.2 (Glycine max), 3'ss of exon 2
------------------------------gt-ttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctctta---tccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
|| || | | || | | ||| | ||| | | | | | | | || | |||||||||||||||||||| ||| | |||||||| |||||||| || ||||| || ||||| || || ||||||
cttgctattcagaatcattaattagcaaatgtattatacacgccagttctaattggttggtggtatactgtactgatgtttgtgatgtgtttgtttgcagCGTTTTGCTGCTGTGATTATGAGGATAAGAGATCCCAAAACAACTGCTCTAATTTTTGCTTCTGGCAAGATG
upper sequence: EFJ17606 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
||| ||| | | | | ||| | | |||||| | | | | | | | | |||||||||||||| || |||||| | ||||| || || |||||||||||| | || ||||| || |||||||||
gatcaacatcttaaccttgttcctattggaggaattttttttctttccctatttgttgccagttttttttatgtattttaaatttatgatgttcctgcagCGTTTTGCTGCCGTAATCATGAGGATAAGGGACCCAAAAACCACGGCTTTGATATTTGCTTCTGGAAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttttttttctcttgtttttatgacttgtctctctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
ttttctcttgttttta CT-rich tract
ttgtttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttgtgttcttttttttctcttgtttttatgacttgtctctctctctcttctcttatccagCGTTTTGCTGCTGTGATCATGCGTATAAGAGAACCCAAAACCACGGCTCTCATCTTTGCGTCCGGAAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG