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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttaaaagcctcggtggtagggttttagttttttaaagataatttagtcggaagttgccgtttacctcgcattaacagaggcatttattcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG

Basic information

species Physcomitrella patens
transcript PP1S197_12V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv12s0028g01210.t01 (Vitis vinifera), 3'ss of exon 4
tgtttaaaagcctcggtggtagggttttagttttttaaagataatttagtcggaagttgccg-tttacctcgcattaacagaggcatttattcgtaaac------agATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG
  | ||||| | |     | ||  | ||  | |    ||  || | |   |  ||||| ||  |||       || |         |  |||  | ||       |||| || |||||||||||||| ||| |||| || |||||||||||||| ||||| ||||| ||||| ||
-ctctaaaaacat-----gcagcctattcatctaaccaac-tactatctccataagtttcctctttgtgctatatcactttgatattccatttttcaattgttttagATTGCGATGAAAGAACTTCGTGAGAGGAAGATACCCTTCACCATTCGGCGCTACCTGCCTGATGGAAG

upper sequence: PP1S197_12V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 6
tgtttaaaagc-ctcggtggtagggttttagttttttaaagataatttagtcggaagttgccgtttacctcgcattaacagaggcatttattcgtaaa-------cagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG
 | ||  |||| |||  |  |   || |      | ||    |||||    |  ||||| ||  |     |    | ||   |  |||  || ||  |        |||| || ||||| |||||||| |||||||| || ||||||||||| || ||||| ||||| ||||| ||
-gattggaagcactcattcatttcgtctg----ctgtaccactaattc---cacaagtttcccctctgtgcttcatgactctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
















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|37853644|gb|BJ611652.1|BJ611652
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATCCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|67691341|gb|BJ951574.1|BJ951574
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|208399259|gb|DC912460.1|DC912460
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|37833887|gb|BJ591899.1|BJ591899
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|162199893|gb|FC376459.1|FC376459
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|67717109|gb|BJ967368.1|BJ967368
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|37841975|gb|BJ599983.1|BJ599983
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATCCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|162251127|gb|FC426404.1|FC426404
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|67508124|gb|BJ940995.1|BJ940995
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|162251128|gb|FC426405.1|FC426405
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|18352449|gb|BJ184503.1|BJ184503
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|162199892|gb|FC376458.1|FC376458
EST:     GATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: GATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|37848516|gb|BJ606524.1|BJ606524
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|208350547|gb|DC926238.1|DC926238
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|18360281|gb|BJ192343.1|BJ192343
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATCCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|18367956|gb|BJ200040.1|BJ200040
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|67725632|gb|BJ975891.1|BJ975891
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC
EST: gi|18364782|gb|BJ196855.1|BJ196855
EST:     TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAG                         ATCGCTATGAAAGAACTTCGGGAGCGGAAAATCCCCTTCACCATTCGTCGC
genomic: TGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGC

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), 34 (downstream exon)
Score: 74

TATGAATGCCCCAGTGATGGTGAATCTAGAAGGCGAGACGGATCCTCTTGAGgtaccttcat ... tcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtcggaagttgccgtttacctcgcattaacagaggcatttattcgtaaacagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG
                          cattaac  putative branch site (score: 74)
                                        tttattc  putative PPT
                                       atttatt  TA-rich tract