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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcgtgcttaggcatagagtttctcagaataatgcatttcatgttgtgttagatgcaaactcgttttcaagtaccgattatttgaagtattgtagttgcattttggtcactgccttctctggattcaacaagatgtgatttgcggtttcagagatgttgctgacaaagttacctctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT

Basic information

species Physcomitrella patens
transcript PP1S246_34V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
gtaatttcgtgcttaggcatagagtttctcagaataatgcatttcatgttgtgttagatgcaaactcgttttcaagtaccgattatttgaagtattgtagttgcattttggtcactgccttctctggattcaacaagatgtgatttgcggtttcagagatgttgctgacaaagttacctctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT
      |  |||||  ||      ||||||| |||    | || |      | ||  |   || | |  ||| ||  |     |||||       | || |  ||||||||||  |  ||| |||   |  ||  |  |||  | |  | || |  |   |||  |      | ||     ||||  |||| |||||||||||||| ||||| || || ||||| || |||||||| || ||||| |||||| | |||||| ||||||||  ||| ||||||
-----gtactgcttctgctc----tttctcataat----ctttgctgaaattattgaa---aagcgctattttaaaaattttctattttcccccatttaatc-cattttggtcgtt--cttttctcactataatta--tgtagtgtttgattactaattggttctttg----ggtattatgcttt--agGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
gtaatttcgtgcttaggcatagagtttctcagaataatgcatttcatgttgtgttagatgcaaactcgttttcaagtaccgattatttgaagtattgtagttgcattttggtcactgccttctctggattcaacaagatgtgatttgcggtttcagagatgttgctgacaaagttacctctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT
                                                                           |||| | ||  |||   | |   | |  ||| ||  |   |  ||| |||   |  ||| |  |||  |    | || |  |   ||| ||     | |   ||||      |||| |||||||||||||| ||||| || || ||||| || |||||||| || ||||| |||||| | |||||| ||||||||  ||| ||||||
---------------------------------------------------------------------------gtactgctt--ttgctctttctcaatc-catgttttttgtt--cttttctcactgtaacta--tgttgtgcttgattactaattggttccttgggtattatgctct------agGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
















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|100438401|gb|BY979938.1|BY979938
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTTCA-G                         GACTTCAAAATTCAGAATATTTGT-GGATCATGTGACGTGAAAGT-CCCT
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTT-CAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATT-GTTGGATCATGTGACGTGAA-GTTCCCT
EST: gi|100441350|gb|BY962639.1|BY962639
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
EST: gi|208354942|gb|DC914206.1|DC914206
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
EST: gi|208376207|gb|DC910783.1|DC910783
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAAGTTNCCTAT
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAA-GTTCCCTAT
EST: gi|208373747|gb|DC936560.1|DC936560
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
EST: gi|208360850|gb|DC934746.1|DC934746
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
EST: gi|100430149|gb|BY978271.1|BY978271
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
EST: gi|208382418|gb|DC927952.1|DC927952
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
EST: gi|100410692|gb|BY992221.1|BY992221
EST:     TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAG                         GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC
genomic: TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATC

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: 26 (upstream exon), 33 (downstream exon)
Score: 6

TATGCTCGCATCATTCAAAAGCTTGGCTTTCAAGCTCATTTCAAGgtaatttcgt ... ctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatgtgatttgcggtttcagagatgttgctgacaaagttacctctctttgcagGACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT
                            tgctgac  putative branch site (score: 6)
                                       ttacctctctttgc  putative PPT
                                   aaagtta  TA-rich tract