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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttctggatagtttcttgcctgtagaatatttagccatgattcgatgtatgcgagacactcatcagtgttgccttgttttttcaaaaaaatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATTAAG

Basic information

species Physcomitrella patens
transcript PP1S1_478V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_478V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 8
-------agc-ttctggatagtttcttgcctgtagaatatttagccatgattcgatgtatgcgagacactcatcagtgttgccttgttttttcaaaaaaatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATTAAG
       ||   |||  |||  ||||| ||   |    |  | |  ||| ||   |  ||   |||     |  | |  |   ||  || ||        |  | ||||| || ||||||||  ||||||||||||||||||||||  | || ||| | |||
accggttagtgctctttataaattcttcccctcactgcaagtggaaatggtttactagatagaagagttgaactaataat--tttaattatt------gtttttccagGGTATTGCACTCATCATCACAGTTCTTCAGATCGTTCGTGTTCCTAATCTCAAG
















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|162277631|gb|FC453262.1|FC453262
EST:     TATGCCTGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: TATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|37850157|gb|BJ608165.1|BJ608165
EST:     TTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: TTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|162160845|gb|FC337667.1|FC337667
EST:     GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|37841043|gb|BJ599051.1|BJ599051
EST:     TGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: TGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|208385472|gb|DC953091.1|DC953091
EST:     GTCAGGACGNTCTT                         GGGATGGCACTCA-TCTCACAGTT-TTCAGATCGTTCGACTGCCAAATATT
genomic: GTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|208370567|gb|DC951603.1|DC951603
EST:     TTGAA-TCCTATGCCTGGATTGGTCAGGACGTTTTT                         GGGATGGCACTCANTCTCACAGTT-NTCAGATCGTTCGACTGCCAAATATT
genomic: TTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|162163486|gb|FC340020.1|FC340020
EST:     GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|208394841|gb|DC915634.1|DC915634
EST:     TTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: TTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|67725738|gb|BJ975997.1|BJ975997
EST:     GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
EST: gi|162212457|gb|FC388705.1|FC388705
EST:     GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTT                         GGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT
genomic: GGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATT

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: 25 (upstream exon), 28 (downstream exon)
Score: 8

TGTCCTTGCTCTGTTTCTCTCGCCCTTTTGTCTCGCGTTTTCCGTTGTTTGGGGCGTTTTCCGTTTGAACTCCTATGCCTGGATTGGTCAGGACGTTCTTgtaagttttc ... aatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtatgcgagacactcatcagtgttgccttgttttttcaaaaaaatcgtgcagGGGATGGCACTCATTCTCACAGTTCTTCAGATCGTTCGACTGCCAAATATTAAG
                              ttgttttttcaaaaaa  TA-rich tract