Sequence
atgc intronic sequence ATGC exonic sequencegtatgctcgcgctggcccatttgatgcttccggactcgtcgatgtgaccgtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP04344 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP04344 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
------------------------gtatgctcgcgctggcccatttgatgcttccggactcgtcgatgtgaccg-tcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
| | | | |||| | || || | | | | | | || | ||| | |||||| ||||| || || ||||| || |||||||| || || | ||||||| || |||||||||||||||||||| || ||||| ||||| ||||||||
ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
upper sequence: EDP04344 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 1
------------------------gtatgctcgcgctggcccatttgatgcttccggactcgtcgatgtgaccgtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
| || | || | ||||| ||| | | ||| || || |||| | | |||||| || || || ||||||||||| ||||| || ||||| || || || ||||| ||||||||| | || ||||| ||||| |||||||| || || |||
gtcagtctcaccttccaaaccctcttgtgttttattggggttttgtgatgtttctaatggtctgggtgttttggttt-gcgatcttct---ctgtgcagAGTGTTCTTGGGATTATTCTGGGAGGTGGAGCAGGCACGCGGCTCTACCCTCTTACCAAGAAGAGGGCGAAGCCTGCGGTTCCCCTGGGGGCGAATTATA
upper sequence: EDP04344 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------gtatgctcgcgctggccca---tttg-atgcttccggactcg--tcgatgtgacc-gtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
| | || || | | |||| || | | | | | || | | || | |||||| ||||| ||||| ||||| ||||| || || || || ||| |||||||| ||||||| |||||||||||||| || ||||| | || ||||| || |
agtgagaaatgtttgctacttttcttacgtctgaatagtgtttgtgtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
upper sequence: EDP04344 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------gtatgctcgcgctgg--cccatttg--atgcttccggactcgtcga--tgtgaccgtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
| || | | | ||| | ||| || | | || | || | | | |||| |||||| || || || || ||||| |||||||| || || | || || ||||| | || ||||||||||| ||||| || ||||| |||||||||||||| |
tgcatgatcttgagatttgagaatcttgtgtcgagatccaatcagaatgttttattaattaatgagctttggcaaacattcttctatgttggttttgcagAGTGTACTAGGAATCATTCTTGGTGGTGGAGCAGGAAGTCGACTTTATCCATTAACTAAGAAGCGTGCGAAGCCAGCCGTGCCACTGGGCGCCAACTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatgcttccggactcgtcgatgtgaccgtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
atttgat putative branch site (score: 5)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctcgcgctggcccatttgatgcttccggactcgtcgatgtgaccgtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC