Sequence
atgc intronic sequence ATGC exonic sequence...gtcacgtcacactctccggctcgccaccgccgcccctcctaatctgcctacatctcgcaccgacgccgcccacccccacccccacactcacgccacgcagGGTGCCCATCCAGGCCTGCATCGGCCAGAAAGTGGTGGCCTCGGAGGCCATTGCGCCCTACCGCAAGGACGTGCTGGCCAAGTGCTACGGCGGCGACATC
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP06216 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP06216 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 19
gtcacgtcacactctccggctcgccaccgccgcccctcctaatctgcctacatctcgcaccgacgccgcccacccccac-ccccacactcacgcca-cgcagGGTGCCCATCCAGGCCTGCATCGGCCAGAAAGTGGTGGCCTCGGAGGCCATTGCGCCCTACCGCAAGGACGTGCTGGCCAAGTGCTACGGCGGCGACATC
| | | | | || | ||| || ||| | | | | | ||||| ||| | || | ||| | ||| || || | || ||||| ||||||||||||||||||||||
--------------------------------------------------------gtgtcacctctttcattttccgtattctacaaaaacaccaacctgagatctctctacagGCGTGCCTTGGGTCTAGAGTCATTGCCAGTGAACAAATCTCAGCCATGCGCAAAGACGTGCTGGCCAAGTGCTACG-----------
upper sequence: EDP06216 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 19
--gtcacgtca--cactctccg-gctcgccaccgccgcccctcctaatctgcctacatctcgcaccgacgcc----gcccacccccacccccacactcacgccacgcagGGTGCCCATCCAGGCCTGCATCGGCCAGAAAGTGGTGGCCTCGGAGGCCATTGCGCC-CTACCGCAAGGAC---GTGCTG-GCCAAGTGCTACGGCG-GCGACATC------------------
| ||| || || | |||| || || | | | | |||| | |||| | | | | | | || || || |||| || | | | | | | | | ||| | ||| | | ||| | || | || | ||||| | | | | || || | |
gtgccacctctttcattttccgtattctacataactctaacccatgatctccgtacaggtttcccttgggtttagagtctttgccagtgaacaaacctgagccatgcgcaaagacgtgctggccaagtgcta--cggtctgtgctctcctttcaactctttgtacagCTCTCAAAACTTCTCAATGCTGCAGGAGGAGACATAACGAGCAAGAAGAAGCTGTTGAAGAAACAA
upper sequence: EDP06216 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: EFJ04299 (Selaginella moellendorffii), 3'ss of exon 4
gtcacgtcacactctccggctcgccaccgccgcccctcctaatctgcctacatctcgcaccgacgccgcccacccccac-ccccacactcacgccacgcagGGTGCCCATCCAGGCCTGCATCGGCCAGAAAGTGGTGGCCTCGGAGGCCATTGCGCCCTACCGCAAGGACGTGCTGGCCAAGTGCTACGGCGGCGACATC
| | | | | || | ||| || | | | | | ||||| ||| | || | ||| | ||| || || | || ||||| ||||||||||||||||||||||
--------------------------------------------------------gtgtcacctctttcattttccgtattctacaaaactctaacccgagatctctctacagGCTTGCCTTGGGTCTAGAGTCATTGCCAGTGAACAAATCTCAGCCATGCGCAAAGACGTGCTGGCCAAGTGCTACG----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctacatctcgcaccgacgccgcccacccccacccccacactcacgccacgcagGGTGCCCATCCAGGCCTGCATCGGCCAGAAAGTGGTGGCCTCGGAGGCCATTGCGCCCTACCGCAAGGACGTGCTGGCCAAGTGCTACGGCGGCGACATC
cactcac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcacgtcacactctccggctcgccaccgccgcccctcctaatctgcctacatctcgcaccgacgccgcccacccccacccccacactcacgccacgcagGGTGCCCATCCAGGCCTGCATCGGCCAGAAAGTGGTGGCCTCGGAGGCCATTGCGCCCTACCGCAAGGACGTGCTGGCCAAGTGCTACGGCGGCGACATC
- - - -cacactc
- - - - - - - - - - - - - - - - - - - - - - -gcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -ctcgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acactca