Sequence
atgc intronic sequence ATGC exonic sequence...gtgcaatgcggctagcacgcgctgttgcggcacaccatatggcagcctgttgcccacatcccgtatgccgtggcgccatgcctcttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP05450 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 7
gtgcaatgcggctagcacgcgctgttgcggcacaccatatggca-gcctgttgcccacatcccgtatgccgtggcgccatgcct-cttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG------
|| | | || | | ||| | | | | || | || | | | | | | | | | | ||| ||| |||||| || || ||||||||||| || || ||||| ||||||||||| |||||||| || |||| || || || || || || | || |||||||
-tgtgtttctgcatgtgcagttggtttcctggcttctttctacatactaaatgtttaagtaatgattaacata-tgttaaacttgtttgttcttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAGATAGTCTTGCTTATATTTGTCTCTGGAAAAATTGTTCTGACAGGAGCCA
upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 7
gtgcaatgcggctagcacgcgctgttgcggcacaccatatggca-gcctgttgcccacatcccgtatgccgtggcgccatgcct-cttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG------
|| | | || | | ||| | | | | || | || | | | | | | | | | | ||| ||| |||||| || || ||||||||||| || || ||||| ||||||||||| |||||||| || |||| || || || || || || | || |||||||
-tgtgtttctgcatgtgcagttggtttcctggcttctttctacatactaaatgtttaagtaatgattaacata-tgttaaacttgtttgttcttgttggtagTATGAACCAGAGCTGTTTCCCGGACTAATCTATCGCATGAAGCAACCCAAGATAGTCTTGCTTATATTTGTCTCCGGAAAAATTGTTCTGACAGGAGCCA
upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtgcaatgcggctagcacgcgctgttgcggcacaccatatggcagcctgttgcccacatcccgtatgccgtggcgccatgc-ctcttgctctgcc--ccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG------
| |||| | | | | |||| | || | || | || ||| | | | | ||||| || ||| | | | |||| || || ||| |||| || || | || || | |||||||||||||||||||| |||| ||||||||||| || ||| | || || || |
agaatttaaaatgttacaaa-atgagctgctttaa-gtgcc------taaactatctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 6
gtgcaatgcggctagcacgcgctgtt-gcggcacaccatatggcagcctgttgcccacatcccgtatgccgtggcgccatgcctcttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG------
|| | | | | | || || || | | || | | ||| | | || || | | || | ||||||| || |||||||| || || | |||||||| ||||||||||| ||||| ||||| ||||||||||| || || ||| | ||||| || |
-----------------------gtaagtcgtgcttcctttgtcacacttacactcttttctcttttgcgg--gtcttatcactaaagttttgt---gcagTACGAACCAGAGCTGTTCCCCGGATTGATCTACCGAATGAAGCAGCCTAAGATCGTGCTCCTGATCTTCGTCTCTGGAAAGATTGTGCTTACTGGTGCAA
upper sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 6
gtgcaatgcggctagcacgcgctgtt-gcggcacaccatatggcagcctgttgcccacatcccgtatgccgtggcgccatgcctcttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG------
|| | | | | | || || || | | | || | | ||| | | || || | | || | ||||||| || |||||||| || || | |||||||| ||||||||||| ||||| ||||| ||||||||||| || || ||| | ||||| || |
-----------------------gtaagtcgtgcttcctttgtcacacttatactcttttctcttttgcgg--gtcttatcactaaagttttgt---gcagTACGAACCAGAGCTGTTCCCCGGATTGATCTACCGAATGAAGCAGCCTAAGATCGTGCTCCTGATCTTCGTCTCTGGAAAGATTGTGCTTACTGGTGCAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|15702725|gb|BI727030.1|BI727030EST: TCCCCATCCGCTTGGAGGGCCTGGCGTACGCGCACAGTCTCTTCGCCAGC TACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAG
genomic: TCCCCATCCGCTTGGAGGGCCTGGCGTACGCGCACAGTCTCTTCGCCAGCgtaagcagtg ... tgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctgttgcccacatcccgtatgccgtggcgccatgcctcttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG
cctcttgctctgcccc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaatgcggctagcacgcgctgttgcggcacaccatatggcagcctgttgcccacatcccgtatgccgtggcgccatgcctcttgctctgccccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - -cacgcgc
- - - - - - - - - - - - - - - -acaccat
- - - - - - - - - - - - - - - - - - - - - - - - - -gcccaca