Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagtaattttacccagccttcactcgtttaatttttcttcttccttgttttacagAGGAGCAACTAGACTTTCCAGTTTTGTACGCTTCTGCCAAGGAGGGATGGGCTTCTTCTACGTTCACAAAGGCACCAGAAGGAGAACCCACTATGGCTCC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ08344 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 4
------------------------------------gtaagcagtaattttacccagccttcactcgtttaatttttcttcttccttgtttt------acagAGGAGCAACTAGACTTTCCAGTTTTGTACGCTTCTGCCAAGGAGGGATGGGCTTCTTCTACGTTCACAAAGGCACCAGAAGGAGAACCCACTATGGCTCC
| || | | | | || || | | || |||| || || || ||| | ||||||||||||||||||||| ||| | || |||||||| || || |||||||| ||| |||| || || |||| || | || ||| | |
gtacagaaattgaaatatctgataattatatttatgcttgatggttttgtaatgtaaactccattatctgaaattttattattattttatttgtgtgaatagAGGAGCAACTAGACTTTCCTGTTCTTTATGCTTCTGCTAAAGAAGGATGGGCGTCTACTACATTTACCAAGGATCCTCCTGCTGATGCCAGAAATATGTC
upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 4
---------------------------------gtaagcagtaatttt---acccagccttcactcgtttaatttttcttctt-ccttgttt-----tacagAGGAGCAACTAGACTTTCCAGTTTTGTACGCTTCTGCCAAGGAGGGATGGGCTTCTTCTACGTTCACAAAGGCACCAGAAGGAGAACCCACTATGGCTCC
| | ||||| | | || || | | || |||| || || || ||| || ||||||||||||||||||||| ||| | || |||||||| || || |||||||| ||| | || || || |||| || | || ||| | |
gtacagcaattgaaatatctgatagttatatttatgcttgattattttgtaatgtaaactccattatctgaaatttttttattattttatttgtgtgtatagAGGAGCAACTAGACTTTCCTGTTCTTTATGCTTCTGCTAAAGAAGGATGGGCGTCTACCACATTTACCAAGGATCCTCCTGCTGATGCCAGAAATATGTC
upper sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------gtaagcagtaattttacccagccttca--ctcgtttaatttttcttcttccttgttttacagAGGAGCAACTAGACTTTCCAGTTTTGTACGCTTCTGCCAAGGAGGGATGGGCTTCTTCTACGTTCAC-AAAGGCACCAGAAGGAGAACCCACTATGGCTCC
| | || ||| | | | |||||| | | | ||||||| |||||||||| || || ||||||||| | || ||||||||||| || ||||||||||| || || ||||| ||| | | | ||| | ||
gtgcaagaaatatctgaaatgggaaaaagttccatgaatctagctgcttctgctgtgactttcactggtttatttgttagttagatgatcaaatttgataaattttcttgcattcttgttt--cagAGGAGCAGCTGGATTTTCCAGTTCTCTATGCTTCTGCCAAAGAAGGATGGGCTTCCTCCACCTTCACTAAAAGTCCTCCTGATAATACCAAGAGCATGTC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtaattttacccagccttcactcgtttaatttttcttcttccttgttttacagAGGAGCAACTAGACTTTCCAGTTTTGTACGCTTCTGCCAAGGAGGGATGGGCTTCTTCTACGTTCACAAAGGCACCAGAAGGAGAACCCACTATGGCTCC
gtttaat putative branch site (score: 4)
ccttcactcgtttaat CT-rich tract
tttaatttttcttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagtaattttacccagccttcactcgtttaatttttcttcttccttgttttacagAGGAGCAACTAGACTTTCCAGTTTTGTACGCTTCTGCCAAGGAGGGATGGGCTTCTTCTACGTTCACAAAGGCACCAGAAGGAGAACCCACTATGGCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA