Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaaaagtcgggttcagattggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
Basic information
species | Chlamydomonas reinhardtii |
transcript | EDP06021 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EDP06021 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 1
gtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaa--aagtcgggttcagattggcgcgcgtga-cggctgggcgctaaaccggggccgctgcgcgcaacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
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-----------------ttttgcaata-cgttttgtgtctgacaaaatttacttagatgctgaaaccttctagtgatcgactgcttgatgtcgtagttttacttgtttttttatgtagGAATGAACAAGATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATCGTGAATGAGCTTGAGGTTCAGCACCCGGCTGCTAA
upper sequence: EDP06021 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
gtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaaaagtcgggttcagattggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
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----------gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaacc---ttccagggatcgattgcttgatgttgta--gttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
upper sequence: EDP06021 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ21647 (Selaginella moellendorffii), 3'ss of exon 1
gtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaaaagtcgggttcagattggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgt-----agGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
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------------------------------------------------------------------gtgagtga--atcgagctctttgtttgcgcttgagtgtgagattcctggctcagGCATGAACAAGATGGTGATCAATCACCTGGACAAGCTGTTTGTGACGAATGACGCCGGGACCATCATCGGTGAGCTAGAAGTCCAGCATCCCGCGGCGAG
upper sequence: EDP06021 (Chlamydomonas reinhardtii), 3'ss of exon 1
lower sequence: EFJ33799 (Selaginella moellendorffii), 3'ss of exon 1
gtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaaaagtcgggttcagattggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgt-----agGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
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------------------------------------------------------------------gtgagtga--atcgagctctttgtttgtgcctgagtgtgagattcctggctcagGCATGAACAAGATGGTGATCAATCACCTGGACAAGCTGTTTGTGACGAATGACGCGGGGACCATCATCGGTGAGCTAGAAGTCCAGCATCCCGCGGCGAAMapped 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|16431467|gb|BI996693.1|BI996693EST: AGCGTGCAAGGGCCTGGCGCAGATCACGCGGACTTCGCTTGGGCCAAACG GCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCG
genomic: AGCGTGCAAGGGCCTGGCGCAGATCACGCGGACTTCGCTTGGGCCAAACGgtaatttgat ... caacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCG
EST:
gi|22061196|gb|BQ814132.1|BQ814132EST: AGCGTGCAAGGGCCTGGCGCAGATCACGCGGACTTCGCTTGGGCCAAACG GCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCG
genomic: AGCGTGCAAGGGCCTGGCGCAGATCACGCGGACTTCGCTTGGGCCAAACGgtaatttgat ... caacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
cgctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgatgtcagactggtgtatcatcggtttggctctgcccgaaaagtcgggttcagattggcgcgcgtgacggctgggcgctaaaccggggccgctgcgcgcaacccgtagGCATGAACAAGATGGTCATCAACCACTTGGAAAAGCTGTTTGTGACCAGCGACGCGAGCACTATCGTGAGCGAGCTGGAGGTGCAGCATCCCGCGGCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG