Sequence
atgc intronic sequence ATGC exonic sequence...tgctcttggccatgtgcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP01972 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP01972 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os08g39140.2 (Oryza sativa), 3'ss of exon 2
--tgctcttggccatgtgcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA---------
| || | || || | | | || | ||| ||| | ||| | | | || | ||| |||| ||| ||||| || ||||| ||| ||||||||||| ||||||||||| ||||| ||| |||||| ||||| || ||||| |||||||
aatcacctgaactcctaagttgaactgtgaaatgtgctataaggtgtcctggctctaatgtgttcatttgttattgacaacttgct--catgcttcctgcagTTGGA---------ATACCTTGAAGAGCGCCGCCTCAAGGACCTGATCAAGAAGCACTCTGAGTTTATCAGCTACCCTATCTCTCTATGGACTGAGAAGACCACTGAGA
upper sequence: EDP01972 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G112165_T01 (Zea mays), 3'ss of exon 2
tgct-cttggccatgtgcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA---------
| | || | |||| | || | || | | | || | || || || | | |||||| || || | ||| ||||||||| |||||||| ||| ||||||| ||||||||||||||| ||||||||| |||||||||||| |||||||| || ||||
ggttatttagaaatgtatttagattattctg--tattgaattgttttttctgtgggagctgctggtgttacttg-taatcacatttcaacttctctcttg-------cagCTGGAGTACCTTGAGGAGCGTCGCCTCAAGGATCTGGTCAAGAAGCACTCTGAGTTCATCAGCTACCCCATCTCCCTGTGGACTGAAAAGACAACAGAGA
upper sequence: EDP01972 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G069651_T02 (Zea mays), 3'ss of exon 2
tgctcttggccatgt--gcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcc-cgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA---------
||| | | ||||||| || || | | || | || | | | || | | | | | |||| || | ||| || ||||| |||||||| ||| ||||||| |||||||||||||| ||||||||| |||||||||||| ||||||||||| ||||
-----ttgatttttcaggactgtgtt----cattttctgtgtagttatttgcttttctgtga---aagctgttggtgtttcttgtactcacctttcaacttctctcttgcagTTAGAATACCTTGAGGAGCGTCGCCTCAAGGATTTGGTCAAGAAGCACTCTGAGTTCATCAGCTACCCCATCTCCCTGTGGACCGAAAAGACAACGGAGA
upper sequence: EDP01972 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G012631_T01 (Zea mays), 3'ss of exon 2
tgctcttggccatgtgcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA---------
|||| ||| | | | | | ||| | | | | || | | | ||| || | | | | | ||| ||||||||| |||||||| ||| ||||||| ||| ||||||||||| |||||||||| |||||| ||||| || |||| |||||||
------atatgatgtatctgc-tagacactgctact-tatttttactgtttggctatttataggtctggactcgttcttacaatat-atatgacttttattttctgcagTTGGAGTACCTTGAGGAGCGCCGCCTCAAGGATCTGATCAAGAAGCACTCCGAGTTCATCAGCTACCCAATCTCTCTCTGGATTGAGAAGACCACTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA
tcctcac putative branch site (score: 2)
cccttccatttccacc putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctcttggccatgtgcctgtgttgccccagttaccgcaaagccgcctcctcaccatgggcccatgccgctcggcccttccatttccacccgtcccgcagGAGGACCAGAAGGAGTACCTGGAGGAGCGGCGCATCAAGGACCTGGTCAAGAAGCACAGCGAGTTCATCTCCTACCCCATCTCGCTGTGGACCGAGAAGA
- - - - - catgtgc
- - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - -cgcaaag
- - - - - - - - - - - - - - - - - - - - - - - - -ctcacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccatgc