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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaattctgctgacttttgaatgttgatatcattcttttttaaagcaacctcactttttaaataaccctttgcagttttattatgtcgagtttgttcgatgatcgagcgttcacaaccatttttgtatcttctactttggcaggacttatcaatacaacttcattgatcttactgcgcgctttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG

Basic information

species Physcomitrella patens
transcript PP1S271_80V6.1
intron # 4
splice site 3'
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|208380288|gb|DC919124.1|DC919124
EST:     CCAATGTTCGGGAGCNTGAAGACTTNCTTATCANCGANTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|162245043|gb|FC421569.1|FC421569
EST:     CCAATGTTCGAGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|162183314|gb|FC359229.1|FC359229
EST:     CCAATGTTCGAGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|208357665|gb|DC934117.1|DC934117
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|18330929|gb|BJ162935.1|BJ162935
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGAT
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGAT
EST: gi|18368238|gb|BJ200323.1|BJ200323
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGA
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGA
EST: gi|100452982|gb|CJ975541.1|CJ975541
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTT-GAG
EST: gi|162245042|gb|FC421568.1|FC421568
EST:     CCAATGTTCGAGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|162266011|gb|FC442696.1|FC442696
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|208352193|gb|DC901714.1|DC901714
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGTATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|208367659|gb|DC947365.1|DC947365
EST:     CCAATGTTCGGGAGCCTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|162183315|gb|FC359230.1|FC359230
EST:     CCAATGTTCGAGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|100439177|gb|BY980132.1|BY980132
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|162266010|gb|FC442695.1|FC442695
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|162204856|gb|FC381187.1|FC381187
EST:     CCAATGTTCGAGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
EST: gi|22492731|gb|BU052654.1|BU052654
EST:     CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTG
genomic: CCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTG
EST: gi|18339530|gb|BJ171557.1|BJ171557
EST:     AGCTTGAAGACTTACTTATCAACGACTGCATGTACTCT                         GGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
genomic: AGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG

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: 28 (upstream exon), 32 (downstream exon)
Score: 7

GTGTTGCCTTATGATTTGTTGATGCAACAATTGGATATTTCCAATGTTCGGGAGCTTGAAGACTTACTTATCAACGACTGCATGTACTCTgtaggaattc ... tttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggcaggacttatcaatacaacttcattgatcttactgcgcgctttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG
                               atcttac  putative branch site (score: 7)
           ttatcaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaattctgctgacttttgaatgttgatatcattcttttttaaagcaacctcactttttaaataaccctttgcagttttattatgtcgagtttgttcgatgatcgagcgttcacaaccatttttgtatcttctactttggcaggacttatcaatacaacttcattgatcttactgcgcgctttgtgacagGGCATAGTTAGAGGGAAGCTGGATCAAAGACGTCGTTGTTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA