Sequence
atgc intronic sequence ATGC exonic sequencegtaatcatctttgtttaggagttctcttgaataatttctctttaatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ21562 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
--------------------------------------gtaatcatctttgtttaggagtt--ctcttgaataatttctctttaatctttaatctt-tagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
| | ||| || | || || | | | ||| | | || | | || ||| || ||||| || | ||||| |||||||| || || || ||||| ||| | || |||||||| || ||||||||||||||||| |||||||| |||
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaagaattgacacccttttgttttgtgaacatgtttcacttttgcagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG
upper sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------gtaatcatctttgtttaggagttctcttg-aataatttctctttaatct---ttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
| | |||| | | || ||||| ||| || | ||| | |||||| ||||| || | |||||||| ||||| || || || ||||| || || |||||||||||||||||||| || |||||||| ||||||||||||
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
upper sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------------------------------gtaatcatctttgtttaggagttctcttgaataatttctctttaatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
| | | |||| | ||| | || | | | ||| |||| ||||||||||| ||||||||| | ||||| || ||||| | || || ||||| || || ||||| || || |||||||| || ||||| || ||||||||||||
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttt--tctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
upper sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------gtaatcatctttgtttaggagttctcttg-aataatttctctt---taatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
| | |||| | | | || ||||| || || | ||| | |||||| ||||| || | ||||| || ||||| || || || ||||| || || |||||||| || |||||||| || |||||||| ||||||||||||
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
upper sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------gtaatcat-ctttgtttaggagttctcttgaataatttctctttaatctttaatcttt---agGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
||| || | ||| ||| | | | || | || |||| ||| |||||| ||||| || |||||||||| ||||| || || || || || ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||
gtaatgaccccactcttctttccaaaaagtagtctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
upper sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv08s0058g01400.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------gtaatcatctttgtt--tagg--agttctcttgaataatttctctttaatctttaatcttt--agGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
||| || || ||| |||| || | | | || ||||| || | || | |||||| || || || | |||||||| ||||| || || || || || ||| | || || || || || |||||||| |||||||||||||||||||||
cttgcctgcacaccaccccccctcccctcttctgggtacacacattggttgctaggctggtattgctctttccttcctcttactactgacacctgtgcagGTGCCAACGATGTTTCAATGATTCAAATGGCAGATGTTGGTGTGGGAATATGTGGTCAGGAGGGGCGTCAAGCAGTAATGGCATCGGATTTTGCAATGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctttgtttaggagttctcttgaataatttctctttaatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
ctttaat putative branch site (score: 4)
tttctctttaatcttt CT-rich tract
aataatttctctttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcatctttgtttaggagttctcttgaataatttctctttaatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG