Sequence
atgc intronic sequence ATGC exonic sequence...tacatcgcccccgaaccccaccgcccaactcagcaatgaacacgcacgcaactaactcactaaccccaacccccgccgccacccggccccccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGACGCCATCGTCGAGGGCTTCGCCGCCAAGTACGGCGCCCGCTTCGCCATGG
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP06351 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP06351 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: LOC_Os05g33570.2 (Oryza sativa), 3'ss of exon 2
----------------tacatcgcccccgaaccccaccgcccaactcagcaatgaacacgcacgcaactaactcactaaccccaacccccg-ccg--ccacccggccccccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGACGCCATCGTCGAGGGCTTCGCCGCCAAGTACGGCGCCCGCTTCGC-CATGG
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gtgcgtatcacttacttatatttactctctctctctcttcct--ctctgccacgccggcg-atgtgacagatcgattgatctccgttgctgatcgatccgtgcgtgcgtgtgtgtgcagGTGTCGATGCCGGGGATGATGGACACGGTGCTGAACCTGGGGCTGAACGACGAGGTGGCGGCGGGACTGGCGGCCAAGAGCGGCGACCGCTTCGCGTACG-
upper sequence: EDP06351 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ27128 (Selaginella moellendorffii), 3'ss of exon 2
tacatcgcccccgaaccccaccgcccaactcagcaatgaacacgcacgcaactaactcactaaccccaacccccgccgccacccggccccccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGACGCCATCGTCGAGGGCTTCGCCGCCAAGTACGGCGCCCGCTTCGC-CATGG
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----------------------------gttagtgtttctagcttttatt-ctttctcggttctgcagggtggtgttagtgttgactgtatgaaatgcagTTGTCAATGCCGGGAATGATGGACACGGTGTTAAATCTGGGGCTCAACGACGAGGTTGCTGCCGGCCTAGGCCAGATAAGCGGCGAGAGATTTGCGTATG-
upper sequence: EDP06351 (Chlamydomonas reinhardtii), 3'ss of exon 3
lower sequence: EFJ33526 (Selaginella moellendorffii), 3'ss of exon 3
tacatcgcccccgaaccccaccgcccaactcagcaatgaacacgcacgcaactaactcactaaccccaacccccgccgccacccggccccccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGACGCCATCGTCGAGGGCTTCGCCGCCAAGTACGGCGCCCGCTTCGC-CATGG
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----------------------------gttagtgtttctagcttttatt-ctttctcggttctgcagggtggtgttagtgttgactgtatgaaatgcagGTGTCAATGCCGGGAATGATGGACACGGTGTTAAATCTGGGGCTCAACGACGAGGTTGCTGCCGGCCTAGGCCAGATAAGCGGCGAGAGATTTGCGTATG-Mapped 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|239842173|gb|GR284030.1|GR284030EST: TCGGAGACGTCAACACGCCGCTGCTGGTGTCCGTACGCTCCGGCGCCGCG GTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGAC
genomic: TCGGAGACGTCAACACGCCGCTGCTGGTGTCCGTACGCTCCGGCGCCGCGgtgagtgtga ... ccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgcaactaactcactaaccccaacccccgccgccacccggccccccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGACGCCATCGTCGAGGGCTTCGCCGCCAAGTACGGCGCCCGCTTCGCCATGG
cactaac putative branch site (score: 1)
ccccccaccccc 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatcgcccccgaaccccaccgcccaactcagcaatgaacacgcacgcaactaactcactaaccccaacccccgccgccacccggccccccacccccagGTGTCCATGCCGGGCATGATGGACACGGTGCTGAACCTGGGCCTCAACGACGCCATCGTCGAGGGCTTCGCCGCCAAGTACGGCGCCCGCTTCGCCATGG
- - - - - - -aacccca
- - - - - - - - - - - - -caactca
- - - - - - - - - - - - - - - - - - - -acacgca
- - - - - - - - - - - - - - - - - - - - - - - - -aactaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcactaa