Sequence
atgc intronic sequence ATGC exonic sequencegtaggcactcgcttccaccttgctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtcacagAGAAATGTAGGATTGGATCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ30650 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ30650 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------gtaggcact----cgcttccaccttgctcaaaaacatcttttgctggccc-------ctggctgaatctctcctgttgtcacagAGAAATGTAGGATTGG---------ATCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
|| || | | | | ||| | | | | | ||| || || | || || |||| || ||||| || | ||| | |||| || |||||||| |||||||||||||| |||||||| |||||||||| || ||||| |
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG---------
upper sequence: EFJ30650 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------gtaggcactcgcttccaccttg---ctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtcacagAGAAATGTAGGATTGGA---------TCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
| |||| || | || ||| ||| | | ||| || |||| ||| | ||||| ||| | |||| | || | | || | | | |||||||| || ||||| |||||||||||||||||||| || | || ||||| |
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtcc----attgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
upper sequence: EFJ30650 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------gtaggcactcgcttccaccttgctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtcacagAGAAATGTAGGATT-GGATCAGC--------AGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
||| || | | | ||| || | | | | | || ||||| || | || | | | |||||||||| | ||||||||||| | |||||||||||||||||| || || | || ||||| |
gtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgcaacagATCTTTGCAAAATCCAGGCCGACTCAAATGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG---------
upper sequence: EFJ30650 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtaggcactcgcttccacct-tgctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtca----cagAGAAATGTAGGATTGG---------ATCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
| | | | | | | | | || | | | | | |||| | || | | ||||| || || ||||| | | | | || | ||| |||||||| |||||||||||||||||||| || || || |||| || | ||| |
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------
upper sequence: EFJ30650 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------gtaggcactcgcttccaccttgc--tcaaaaacatcttttgctg-gcccctggctgaatctctcc--tgttgtca-cagAGAAATGTAGGATTGG---------ATCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
|| | | || |||| | | | | | || | | || | | | || ||| |||| |||| || |||||||| | ||| | |||| ||| |||||||| ||||||||||| ||||| ||||||||| | || | ||| | ||| |
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcatcagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtcacagAGAAATGTAGGATTGGATCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
tctctcctgttgtc CT-rich tract
aaaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcactcgcttccaccttgctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtcacagAGAAATGTAGGATTGGATCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA