Sequence
atgc intronic sequence ATGC exonic sequencegtctttcaaagcatttattcgctcaagttctcatggtaaaacgcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ08416 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
----------------------gtctttca--aagcatttattcg--ctcaagttctcatggtaaaacgcgtgc--------------agGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG
| ||| | | || | || || | | ||| ||| | | | ||||||||||||||||||| ||||| | |||||||| |||||||| || |||| || || || |||||| |||| ||| | ||||| ||||| | ||
gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------gtctttcaaagcat--ttattcgctcaagttctcatggtaaaacg-cgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG
|| | | | ||| | | | || ||| | |||||||||| ||||||| |||||||| |||| |||||||||||| | |||||| || || | | || ||| ||||| |||||| ||||| | |||
gttcacttcaaaatcaatttttgcaaatgttcattcaatggcactaaatcctatgtggtttggttagtacttagtactaacaaattaagttaacaagcagGAGAAGTTGCCACCGACAGATTCAAGACTAAGACCTGATCAAAGGTGTTTGGAGAATGGACAGCATGAAATGGCCAATTCTGAAAAGTTGCGGCTGGAAC
upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------------------gtctttcaaagcatttattcgctcaagttctcatggtaaaacgcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG
|| || || | | || | || | || | | | |||| |||||||| ||||||||||| | || |||| ||||||||||| ||||| ||||||||||| ||| |||| ||| || || | | |||||
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttc-gtaattttgttcccttggtttaagGAAAAGCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGA
upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------------------gtctttcaaagcatttattcgctcaagttctcatggtaaaacgcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG------
|| || || | | || | || | || | | | |||| |||||||| ||||||||||| | || |||| ||||||||||| ||||| ||||||||||| ||| |||| ||| || || | | |||||
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgttttagcaactgtgtgatcttttc-gtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctttcaaagcatttattcgctcaagttctcatggtaaaacgcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG
atttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttcaaagcatttattcgctcaagttctcatggtaaaacgcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC