Sequence
atgc intronic sequence ATGC exonic sequencegtgacgccacgctcaccctcagtttacggggcgcagtcacgtaggcttcatagtatttggggcgtcggagaggtccagtgtgacctgaagaatggcctgggctgcggtatcaacacgcgggcgttgttggagctgcaatgtgaacgcggatgtccctcacaggtccctcacgggatccctccttggctcggccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCACGCCCATCCTGGAGAAGGTCTGCCAGTACTTTTACTACAAACTGCGCTA
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDO98353 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDO98353 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: LOC_Os11g48030.1 (Oryza sativa), 3'ss of exon 1
gtgacgccacgctcaccctcagtttacggggcgcagtcacgtaggcttcatagtatttggggcgtcggagaggtccagtgtgacctgaagaatggcctgggctgcggtatcaacacgcgggcgttgttggagctgcaatgtgaacgcggatgtccctcacaggtccctcacgggatccctccttggctcggccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCACGCCCATCCTGGAGAAGGTCTGCCAGTACTTTTACTACAAACTGCGCTA
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------------------------------------------------------------------------------------------------gttcgtctccttccccatctatcgatccgattcgctttgctttctcaaaccctagattgcct-tgaattatccaccaaatccaaat---------ccaacacagGCGGCTTCTCCGAGACGCGCGAGGGCGAGGTTAGGTTCCCCGAGATCAGCACCCCCATCCTCGAGAAGATCTGCCAGTACTTCTACTGGTCGCTCCACTA
upper sequence: EDO98353 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: PP1S424_27V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgacgccacgctcaccctcagtttacggggcgcagtcacgtaggcttcatagtatttggggcgtcggagaggtccagtgtgacctgaagaatggcctgggctgcggtatcaacacgcgggcgttgttggagctgcaatgtgaacgcggatgtccctcacaggtccctcacgggatccctccttggctcggccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCACGCCCATCCTGGAGAAGGTCTGCCAGTACTTTTACTACAAACTGCGCTA
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---------------------------------------------------------------------------------------------tgactgggttcagggggcga---gtcgtcatcactagtatttatacttttacagaaaagattttcagtaagttttgagcaaat---taattggagtt-ctgacacagGGAACTTCACGGAAACGGAGTTGGGAGAAGTGAAGTTTCCGGAAATCAGTACACCCATTTTGGAGAAGGTGTGCCAGTACTTTTACTGGTCCTTGCAATTMapped 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|14229441|gb|BG848257.1|BG848257EST: CAAGGCCGCGTGCGTGTCCAACACCATCCGCAACATGCTCAGCTCCCAAG GTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCA
genomic: CAAGGCCGCGTGCGTGTCCAACACCATCCGCAACATGCTCAGCTCCCAAGgtgacgccac ... gccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCA
EST:
gi|7427422|gb|AW661588.1|AW661588EST: CAAGGCCGCGTGCGTGTCCAACACCATCCGCAACATGCTCAGCTCCCAAG GTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCA
genomic: CAAGGCCGCGTGCGTGTCCAACACCATCCGCAACATGCTCAGCTCCCAAGgtgacgccac ... gccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCA
EST:
gi|8933125|gb|BE227886.1|BE227886EST: CAAGGCCGCGTGCGTGTCCAACACCATCCGCAACATGCTCAGCTCCCAAG GTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCA
genomic: CAAGGCCGCGTGCGTGTCCAACACCATCCGCAACATGCTCAGCTCCCAAGgtgacgccac ... gccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcggatgtccctcacaggtccctcacgggatccctccttggctcggccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCACGCCCATCCTGGAGAAGGTCTGCCAGTACTTTTACTACAAACTGCGCTA
ccctcac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacgccacgctcaccctcagtttacggggcgcagtcacgtaggcttcatagtatttggggcgtcggagaggtccagtgtgacctgaagaatggcctgggctgcggtatcaacacgcgggcgttgttggagctgcaatgtgaacgcggatgtccctcacaggtccctcacgggatccctccttggctcggccgccgcagGTAGCTTCACGGAGACGGAGCTGGGCGAGGTGAAGTTCCCGGAGATCTCCACGCCCATCCTGGAGAAGGTCTGCCAGTACTTTTACTACAAACTGCGCTA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA