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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtctttgtcatgacttgtttttgtttcgaagttttccacctcttggtttggattggtattggcgtggtccctgaccatgaaaccttgggtttgtggaattagggtcctgtcctggctcaaattgacaaaaggcatatttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAGGAAGCGCATTAAGTTGAGTTCCGAGAAGGCCATCTTCATCTTTGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S209_114V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S209_114V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G014975_T01 (Zea mays), 3'ss of exon 2
gtaggtctttgtcatgacttgtttttgtttcgaagttttccacctcttggtttggattggtattggcgtggtccctgaccatgaaaccttgggtttgtggaattagggtcctgtcctggctcaaattgacaaaaggc-atatttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAGGAAGCGCATTAAGTTGAGTTCCGAGAAGGCCATCTTCATCTTTGTGAAG
                                                    |  |    |   |  |     | ||   ||     |  |           ||   |        || ||| || | |||   |      |   |||||||| ||||| || || ||  | ||||| ||||||||||| |||||  |  |||||||||| ||| | ||  |||||||||| ||||||||||| ||||||
--------------------------------------------------cattaaccaattcagaaggaactcttgcttatcggtacaagccaagaccagcttgcagcatctgtgtgcctccaagtaacatgcgattgcttgcatgcagGTACCTTGTCCCCGCCGACCTCACAGTGGGACAGTTTGTGTACGTGGTGCGGAAGCGCATCAAGCTCAGCGCCGAGAAGGCGATCTTCATCTTCGTGAAG
















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|67575443|gb|BJ948267.1|BJ948267
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162233637|gb|FC409396.1|FC409396
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162266942|gb|FC443030.1|FC443030
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162225361|gb|FC401165.1|FC401165
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|100416767|gb|BY993077.1|BY993077
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162238593|gb|FC418163.1|FC418163
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|67698910|gb|BJ959143.1|BJ959143
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|100386838|gb|BY988107.1|BY988107
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162200693|gb|FC377876.1|FC377876
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162215669|gb|FC391709.1|FC391709
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|18331879|gb|BJ163891.1|BJ163891
EST:     ACATACCAGACATCGATAANAAAAA                         GTATCTTGTCCCAGCTGATTTAACAGNCGGACAGTTTGTATACGTCATAAG
genomic: ACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162264864|gb|FC440639.1|FC440639
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162225362|gb|FC401166.1|FC401166
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162246388|gb|FC422420.1|FC422420
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162200692|gb|FC377875.1|FC377875
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|18339800|gb|BJ171827.1|BJ171827
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|37830291|gb|BJ588303.1|BJ588303
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTNNCAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162246361|gb|FC422419.1|FC422419
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162173286|gb|FC350068.1|FC350068
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCACACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162262384|gb|FC437711.1|FC437711
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162233638|gb|FC409397.1|FC409397
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162173285|gb|FC350067.1|FC350067
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162215670|gb|FC391710.1|FC391710
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162266941|gb|FC443029.1|FC443029
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162270438|gb|FC447554.1|FC447554
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|6102504|gb|AW126974.1|AW126974
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATNCTTGTACC
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTAT-CTTGTACC
EST: gi|18350954|gb|BJ183005.1|BJ183005
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162238594|gb|FC418164.1|FC418164
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
EST: gi|162216854|gb|FC393036.1|FC393036
EST:     ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAA                         GTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG
genomic: ATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 71

AGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAATCCCAGTGATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGATAAGAAAAAgtaggtcttt ... atttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAGGAAGCGCATTAAGTTGAGTTCCGAGAAGGCCATCTTCATCTTTGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggaattagggtcctgtcctggctcaaattgacaaaaggcatatttgtgcagGTATCTTGTACCAGCTGATTTAACAGTCGGACAGTTTGTATACGTCATAAGGAAGCGCATTAAGTTGAGTTCCGAGAAGGCCATCTTCATCTTTGTGAAG
                             aattgac  putative branch site (score: 71)
                                           atatttgt  TA-rich tract