Sequence
atgc intronic sequence ATGC exonic sequencegtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ18166 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------gtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTT---TCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------
| | ||| | | | | || || ||| | | | | |||| | || |||||||| |||||||||||||| || ||||||||||||||||| | ||||| || || || ||||| ||||| || ||||
gaaattatggaaacagagaactgctggaatgaatacctcataggcagttatgtaccaaatttgtctacatgtt-ctcattaatgtacaatctcttgtttagGGCCTTGTCAAACTTGCTGATTTTGGAGTTGCTACTAAATTAACTGAAGCTGATATCAACACACATTCAGTGGTTGGAACTCCATACTGGATGGCCCCTG
upper sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G305321_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------gtgtttac-tacttgagcca-gtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------
| | | | || | | | ||| || | | | | || |||| | || |||||||| ||||||||||||||||| ||||| |||||||||||| | |||||||| || || || || ||||| || ||||
ttgtgaagtgtgtatcccccttaattctaaacttgcaatagaaacatagcagtaatatgttttctctacatatcttcatttatga-accctgcttgtttagGGTCTTGTCAAACTTGCTGATTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
upper sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G017654_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------gtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTT--TCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------
|| |||| | | | | | |||| | |||| | || |||||||| || |||||||||||||| ||||| |||||||||||| | |||||||| || || || || ||||| || ||||
atatgaaatatgtatccccctttattctaaacttccaatagaaacataacaataacactttttctctacatatcttcatttgtgtaccctgcttgtttagGGCCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTCGGCACTCCATACTGGATGGCGCCTG
upper sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv01s0011g02270.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------gtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------
| | | | | | | | ||||| || | | || |||||||| | || |||||||| || ||||| ||||| || ||||||||||| || || || || || || |||||||||||||| || |||||||
cattttatatgaaacttaagctcacaatttgtttggaatggtataggagcttctggatggattttcttaagtaattgcttga--actgatttata---ttttcagGGTCTTGTGAAACTTGCTGACTTTGGTGTTGCAACAAAATTAACTGAGGCAGATGTTAATACGCATTCCGTTGTTGGGACACCATATTGGATGGCCCCTG
upper sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S66_286V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------------------------------------------------gtgtttac-tacttgagccagtggcttgcttgctaacatgtagAGCTTT----CAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------
| ||| || || | | | ||| ||| | | | ||||| || ||||| || |||||||||||||||||||||||||| || |||||| | |||||||| || |||||||| ||||| |||||||
gtagaatacttaccctttgggtcgagctgctcttaaattgcaatcttttgaataccttgccgagtaacgtgtcctgtagttttatttgtagattttttgcttttgtgtatctggaactgcatgtctgatgccttgatggaaattgtctaaacagGGGGAGGTGAAACTCGCAGATTTTGGAGTTGCCACCAAATTAACCGAGGCTGACATCAACACTCATTCTGTTGTTGGCACTCCTTATTGGATGGCTCCTG
upper sequence: EFJ18166 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S131_142V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------------------------gtgtttactacttgagccagt---ggcttgctt----gctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA---------
| |||| | | || | | | | | | || ||| | | | | ||||| |||||||| || |||||||||||||||||||||||||| || |||||| | |||||||| || |||||||| || || |||||||
gtgggttattcacggtctgagctgtgctgtctaagtttccgttcttttaattatccagctgagttactagtcctctagctctacttacatgttgaggggttttccatatgggaaacttcagacctaattcaatgctggt-tattgtccaaatagGGAGAGGTAAAACTCGCAGATTTTGGAGTTGCCACCAAATTAACCGAGGCTGACATCAACACTCATTCTGTTGTTGGTACACCTTATTGGATGGCTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA
tgctaac putative branch site (score: 1)
tttacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttactacttgagccagtggcttgcttgctaacatgtagAGCTTTCAGGGATTCGTAAAACTTGCGGATTTTGGAGTTGCCACCAAATTAACTGAAGCTGACGTGAACACTCACTCCGTTGTTGGGACTCCGTATTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA