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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatattcatacacattgtaaatcatacactgaacttagacgtgcagatattagtgattgtaagcagctaatttattgcgatgattgtctggtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTACAAGTCTTAGAAATCCTTGATATTCAAGGTTAGTTTACACCAATAGCAAG

Basic information

species Physcomitrella patens
transcript PP1S4_215V6.1
intron # 7
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|22491814|gb|BU051737.1|BU051737
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162264332|gb|FC440498.1|FC440498
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|18333863|gb|BJ165879.1|BJ165879
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|18332708|gb|BJ164721.1|BJ164721
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|19789046|gb|BQ041060.1|BQ041060
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162245009|gb|FC424967.1|FC424967
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|208371352|gb|DC944516.1|DC944516
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|6102388|gb|AW126858.1|AW126858
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162245008|gb|FC424966.1|FC424966
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|67696462|gb|BJ956695.1|BJ956695
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162238938|gb|FC417702.1|FC417702
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162179827|gb|FC356418.1|FC356418
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|7584099|gb|AW699997.1|AW699997
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162235909|gb|FC411652.1|FC411652
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
EST: gi|162199674|gb|FC375913.1|FC375913
EST:     ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCA                         ATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC
genomic: ATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTAC

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), 35 (downstream exon)
Score: 23

CAGATTTGAAGATGAAAACACGAAGCTCTCCAGGATGTCTTCGAAATATTGCCTTCCGCTAGTAACCTTGGAGAAATATTCTTGTACTTTTTGCAgtaagttttt ... gtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTACAAGTCTTAGAAATCCTTGATATTCAAGGTTAGTTTACACCAATAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattagtgattgtaagcagctaatttattgcgatgattgtctggtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTACAAGTCTTAGAAATCCTTGATATTCAAGGTTAGTTTACACCAATAGCAAG
                   agctaat  putative branch site (score: 23)
                      taatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatattcatacacattgtaaatcatacactgaacttagacgtgcagatattagtgattgtaagcagctaatttattgcgatgattgtctggtatgtgcagATGCATGGTGCACTGAAGTGGTGATTGCTACAGGTGAGCGGGTTTGTGTACAAGTCTTAGAAATCCTTGATATTCAAGGTTAGTTTACACCAATAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG