Sequence
atgc intronic sequence ATGC exonic sequence...tgtggagtctgcgtacccgtatgcgcacgctcgcgacccgggtgttgatccgtcctgtcccccgcccgccccacaccccccctcccctccgcctgtgcagGTGCCGCGCCGCATGATCGGCACCGACGCCTTCCAGGAGACTCCCAT
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP01876 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP01876 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: LOC_Os04g31960.1 (Oryza sativa), 3'ss of exon 1
----------------------tgtggagtctgcgtacccgtatgcg-cacgctcgcgacccgggtgttgatccgtcctgtcccccgcccgccccacaccccccctcccctccgcc-----tgtgcagGTGCCGCGCCGCATGATCGGCACCGACGCCTTCCAGGAGACTCCCAT-----------------------------------------------------
||| |||||||| || | || | || ||| ||| | || |||| || || ||||| || | || || | | |||| | |||||| |||||||||||||||||||||||||| ||||||||||| |||||
gtacgcgcgctcgtcggggcggcctggcgtctgcgtcgccacctccggcccgggcgccaccaacctcgtg-tccgcgctcgccgacgcccacctcgactccgtcccgctcgtcgccatcacggggcagGTCCCGCGCCGCATGATCGGCACCGACGCGTTCCAGGAGACGCCCATCGTCGAGCTCACCCGCTCCATCACCAAGCACAACTACCTAGTCCTCGACGTCG
upper sequence: EDP01876 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: GLYMA04G37270.1 (Glycine max), 3'ss of exon 1
tgtggagtctgcgtacccgtatgcgcacgctcgcgacccgggtgttgatccgtcctgtcccccgcccgccccacaccccccctcccctccgcctgtgcagGTGCCGCGCCGCATGATCGGCACCGACGCCTTCCAGGAGACTCCCAT-------------------------
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---------------------------------------gtgagcggcctcgccgacgctttaatggacagCGTCCCAGTCGTCGCCATCACCGGC-CAGGTCCCCCGCCGGATGATCGGCACCGACGCCTTCCAAGAAACCCCGATCGGTGGAAGGTGAGCAGATCCATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatccgtcctgtcccccgcccgccccacaccccccctcccctccgcctgtgcagGTGCCGCGCCGCATGATCGGCACCGACGCCTTCCAGGAGACTCCCAT
tgttgat putative branch site (score: 4)
tcccccgcccgcccca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtggagtctgcgtacccgtatgcgcacgctcgcgacccgggtgttgatccgtcctgtcccccgcccgccccacaccccccctcccctccgcctgtgcagGTGCCGCGCCGCATGATCGGCACCGACGCCTTCCAGGAGACTCCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - atgcgca
- - - - - - - - - - - - - - - - - - - -gggtgtt