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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGATCATAGTCACAGTCACGACCATGACCACGACCATGACCACGACCACGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcaccttgcagtggttgtatgttgtgttcaaaaatacatttagttcatgcagggtgggaggatagaatgctctgattttcagtctttatttaat...

Basic information

species Physcomitrella patens
transcript PP1S31_130V6.1
intron # 7
splice site 5'
intron type U2

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|162156786|gb|FC333598.1|FC333598
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162197127|gb|FC372479.1|FC372479
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162157523|gb|FC333781.1|FC333781
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162242561|gb|FC419216.1|FC419216
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162253296|gb|FC428890.1|FC428890
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|208374619|gb|DC948619.1|DC948619
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|208351971|gb|DC925780.1|DC925780
EST:     CGAACACACGCATAAGTGTGAGGAGGATCGTGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162151813|gb|FC328059.1|FC328059
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|18338140|gb|BJ170164.1|BJ170164
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|67725452|gb|BJ975711.1|BJ975711
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162184554|gb|FC360028.1|FC360028
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162195572|gb|FC371873.1|FC371873
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162190694|gb|FC367580.1|FC367580
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|37831922|gb|BJ589934.1|BJ589934
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162162261|gb|FC338043.1|FC338043
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162159886|gb|FC336139.1|FC336139
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162161773|gb|FC338213.1|FC338213
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162178673|gb|FC354462.1|FC354462
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162155636|gb|FC331561.1|FC331561
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162176070|gb|FC351864.1|FC351864
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|208373025|gb|DC948790.1|DC948790
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGATCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162187276|gb|FC363226.1|FC363226
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162155637|gb|FC331562.1|FC331562
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|37827407|gb|BJ585419.1|BJ585419
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162162411|gb|FC339168.1|FC339168
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162162262|gb|FC338044.1|FC338044
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162178674|gb|FC354463.1|FC354463
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|208356256|gb|DC946262.1|DC946262
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162157524|gb|FC333782.1|FC333782
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162190693|gb|FC367579.1|FC367579
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|208364862|gb|DC943680.1|DC943680
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162269789|gb|FC445657.1|FC445657
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
EST: gi|162269788|gb|FC445656.1|FC445656
EST:     CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTG                         GTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT
genomic: CGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCT

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: 33 (upstream exon), 30 (downstream exon)
Score: 19

CATGATCATAGTCACAGTCACGACCATGACCACGACCATGACCACGACCACGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcac ... aattttgcagGTCACAACCATGACCACGACCATGACCATGTGCACGATCCAGGGGTTTCCTCTGTTTCAATAGTGTGTGATGGTGCTCTTGATCTTGACAGG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGATCATAGTCACAGTCACGACCATGACCACGACCATGACCACGACCACGAACACACGCATAAGTGTGAGGAGGATCATGTTCATACTGCTGAGTGTGgtgagtgcaccttgcagtggttgtatgttgtgttcaaaaatacatttagttcatgcagggtgggaggatagaatgctctgattttcagtctttatttaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaata