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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC

Basic information

species Chlamydomonas reinhardtii
transcript EDP04353
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: AC217358.3_FGT008 (Zea mays), 3'ss of exon 1
gcaaggc-tatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
| | |||   |||||| |    |  |  ||||   |   |||  ||   |   || |   |  |    ||||| ||||||||||| ||||||||||| || |||||||| || || |||||||| ||||||||||| || ||||| |||||||| ||||| |  || || |
gtacggcacctctgcatgctctg-ctcaactgtcaactcccaccgatcgatcacggtcacggacca--cagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCCATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
---------------------------------------------------------gcaaggctat--ctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                                                         |   ||| ||  ||||  |    |  |  ||||   |   |||  ||   |   || |   |  |    ||||| ||||||||||| ||||||||||| || |||||||| || || |||||||| |||||||| || || ||||| |||||||| ||||| |  || || |
gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgaccggccggccatgactgcctgctctg-ctcaactgtcaactcccaccgatcgatcacggtcacggacca--cagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
gcaaggctatctgcaagagaggatttgactg-------------gtcatggccattgacaaaatg------cgctgttgc--tctga---------gcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                             ||             |  |  | || | ||     |      | |  ||||    |||           |||| || ||||||| |||||||||||| || |||||||| |||||||||||||| ||||| || || || ||||| ||||| || || ||  | || ||  
nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G154960_T01 (Zea mays), 3'ss of exon 1
--------------------------gcaaggctatct--gcaagagaggatttgactggtcatggcc--attgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                          |   ||||      || |     | | ||  || ||   ||   | |  |    | | || ||  |    |||| | ||||| |||||  ||||||| || || |||||||| ||||| |||||| | ||||||||||| || ||||| |||||| | ||||| |||||||| |
ggaattccttccttactgatggtgttgtttggcttctgaagctactcgtgttatggatgatctcagcagaagttccttttttctcttttatttgaggcagATAGACGGGAAGACTGTCAAGGCACAGATATGGGACACGGCAGGGCAGGAGAGGTACCGCGCCATCACCAGCGCCTACTACAGGGGCGCGGTCGGAGCGC

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S26_33V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------gcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                                  ||    |  ||       | |  || |  | |  | ||   ||   || |  |||||   |   | ||||| || || ||||| || || || || ||||||||||| ||||| |||||| | ||||| |||||||| || || ||||| ||||| || ||||||||  
cgattttttcatctcaaccttgatttggatgatccatcattgcctcttttgcatgtgttaag-gctttttgctgatgtttaagtttgctgt--attatatcagGTTGATGGAAAGACGATTAAAGCTCAGATTTGGGACACAGCAGGACAGGAGAGGTACCGAGCCATTACAAGTGCGTACTATCGTGGAGCCGTCGGAGCTT

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S21_298V6.2 (Physcomitrella patens), 3'ss of exon 2
----------------------------gcaaggctatctgcaagagaggatttga---ctggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                               ||   |   | |    || |||||    ||||   |    | |   |   | |    ||  | | |  |||||||||| ||||||||||| || ||||| ||||| || ||||| |||||| | ||||| || || || || |||||||||||||||||||| ||||| |
ttgacagattttggtcatctagtgatgtcttagatgacgcgtagctaagaatttgttgtctggaagttctaacttttagtgtccttctttatttt-attagGTCGACGGAAAGACCATCAAAGCTCAAATCTGGGATACGGCAGGTCAGGAGAGATACCGAGCTATCACTAGTGCATACTACCGTGGCGCTGTGGGAGCTC

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ30172 (Selaginella moellendorffii), 3'ss of exon 1
-------------------gcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagc---agGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                         || |   ||    |   |    ||    ||||   |||      | | | |  |    || |   |||| || |||||||| ||||| || ||||| |||||||| || || || ||||||||||||||||| || ||||| |||||||| ||||| || || || |
gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggttg-tgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC

upper sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
-------------------gcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagc---agGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                         || |   ||    |   |    ||    ||||   | |      | | | |  |    || |   |||| || |||||||| ||||| || ||||| |||||||| || || || ||||||||||||||||| || ||||| |||||||| ||||| || || || |
gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggt-ggtgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC

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|161804362|gb|FC089704.1|FC089704
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|9459748|gb|BE452889.1|BE452889
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|161815543|gb|FC101788.1|FC101788
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|161798278|gb|FC083487.1|FC083487
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|23363628|gb|BU651448.1|BU651448
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|9459215|gb|BE452496.1|BE452496
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|161821621|gb|FC108746.1|FC108746
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|9441236|gb|BE441840.1|BE441840
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|23359663|gb|BU647483.1|BU647483
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|16071620|gb|BI873616.1|BI873616
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|15701542|gb|BI725847.1|BI725847
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|6541367|gb|AV387151.1|AV387151
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|8828268|gb|BE211998.1|BE211998
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
EST: gi|16073328|gb|BI875324.1|BI875324
EST:     TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAG                         GTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG
genomic: TCGAGTCCAAGTCTACCATTGGCGTGGAGTTCGCGACTCGCAGCATTCAGgcaaggctat ... ctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
                        cattgac  putative branch site (score: 3)
                                          ttgctct  putative PPT
                             acaaaat  TA-rich tract