Sequence
atgc intronic sequence ATGC exonic sequencegtgagcttgactatgtcactacctagaagacttaacgattttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ06179 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------gtgagcttgactatgtcactacctagaagacttaacga-ttttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
| || ||| | | || | | | | | || | | |||||| |||||||| || |||||||| ||||| |||||||| |||||||| || || || ||||| ||||||||||| |||||||| ||||| || || || |
aatggtcatgaacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaattatgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
upper sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G017305_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------gtgagcttgactatg-tcactacctagaag--acttaa---cgattttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
| | || | ||| | ||| ||| | | ||| | |||| | |||||| |||||||| || |||||||| ||||| |||||||| |||||||| || || || ||||| ||||||||||| ||||| || ||||| || || || |
aatgatcatgaacccaaccaatcttttctctcttgtagcctttttcatctggtctaaacttgatacatagtggctaattatgtccacttttccttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCCACCGAATGTGGAACAACAT
upper sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtgagcttgactatgtcactaccta--gaagacttaacg-attttttctgt-----cagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
|||| || | | | | | || |||| | | | ||| ||||||| |||||||| | | || |||||||||||||| |||||||| || ||||| |||||||| || || | || || || || ||||||||||| ||||| || |
ttttaataaagctcataacatatccacacattttgaatctcagtgaa-ttaaatgtcttggtgaatattgaagtttgagctcattatttctgttcttgcagGGAATCAGGAGACCGTGGAAAGGTGTTCTCATGTTTGGACCTCCAGGAACTGGGAAGACACTTCTTGCTAAAGCAGTTGCTACTGAATGTGGGACCACTT
upper sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA15G01510.1 (Glycine max), 3'ss of exon 1
----------------------------------------gtgagcttgactatgtc--actacctagaagacttaacgattttttctgt-------cagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
|| | | | || | | | | || || ||| | ||||| |||||||| | | || |||||||||||||| |||||||| || ||||| |||||||| || || | || || || || ||||||||||| || || || |
tgcttgtgaaattgttgtgacaactgacaagatgaagttcatgcacgtaaatacaatgaagttcattgacaacaatgtaattgtgtctgtgttgctgcagGGAATAAGGAGACCCTGGAAAGGTGTTCTCATGTTTGGACCTCCAGGAACTGGGAAGACGCTTCTTGCTAAAGCAGTTGCTACTGAATGTGGTACCACTT
upper sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------gtgagcttgactatgtcactacctagaagacttaacgatttttt--ctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
| || ||| | | | | | ||| ||| | || ||| | ||||||||| | | ||||||||||||||||| |||||||| || || |||||||| || || || ||||| || || || |||||||| || || || || |
gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagcttgactatgtcactacctagaagacttaacgattttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
acttaac putative branch site (score: 3)
ttttttctgtc putative PPT
attttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcttgactatgtcactacctagaagacttaacgattttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG