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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGGTCGCATGATCCTGAGTTTGAGGAAGATTCAATATGACCTTTGCTGGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaattgactgcctcttaatggataatctctgatcatctaatggttagaacctcatttgcaggtgacctagttttctcttaaataccttagtccc...

Basic information

species Physcomitrella patens
transcript PP1S32_313V6.1
intron # 2
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|19785989|gb|BQ040423.1|BQ040423
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|100361411|gb|BY965827.1|BY965827
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGGACG                         ATCTTGTCGCACAACTCAGGAGGG
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGG
EST: gi|162169717|gb|FC345254.1|FC345254
EST:     GACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|208364552|gb|DC930942.1|DC930942
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGANGGTTTGTTGTAAATGTTGANGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162249173|gb|FC420398.1|FC420398
EST:     GTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162189197|gb|FC366719.1|FC366719
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162156033|gb|FC332200.1|FC332200
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162252958|gb|FC429019.1|FC429019
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162174660|gb|FC351348.1|FC351348
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|18327036|gb|BJ159037.1|BJ159037
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|100426960|gb|BY977451.1|BY977451
EST:     AGCGGTGCGCGCAAAATGT-GGCCTGATGACGTCGTCGTCGAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTG
genomic: AGCGGTGCGCGCAAA-TGTTGGC-TGATGACGTCGTCGTC-AGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTG
EST: gi|162196282|gb|FC375391.1|FC375391
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162167953|gb|FC344891.1|FC344891
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|100433748|gb|BY960687.1|BY960687
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTG
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTG
EST: gi|162187440|gb|FC362662.1|FC362662
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|208380465|gb|DC914889.1|DC914889
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|208365201|gb|DC931167.1|DC931167
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162263939|gb|FC439208.1|FC439208
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|100384235|gb|BY969366.1|BY969366
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCANGAGGGGTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|100387097|gb|BY951496.1|BY951496
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTCANGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGT
EST: gi|162172210|gb|FC348775.1|FC348775
EST:     GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACG                         ATCTTGTCGCACAACTC
genomic: GGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTC

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), 33 (downstream exon)
Score: 36

CAATGGTCGCATGATCCTGAGTTTGAGGAAGATTCAATATGACCTTTGCTGGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaat ... ccgtgtacagATCTTGTCGCACAACTCAGGAGGGTTTGTTGTAGATGTTGAGGGCCTGCGTGGTTTTGTGCCTTTCTCTCAGGTTTCAGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGGTCGCATGATCCTGAGTTTGAGGAAGATTCAATATGACCTTTGCTGGGAGCGGTGCGCGCAAATGTTGGCTGATGACGTCGTCGTCAGGGGAACGgtgggtcaattgactgcctcttaatggataatctctgatcatctaatggttagaacctcatttgcaggtgacctagttttctcttaaataccttagtccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT