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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGGCCGCATGATTTTGAGTTTGAGGAAGATTCAACACGAATTATGCTGGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccatttttttccccgacattcctaatcgctttccagtctttgtagggacatcaagtaagaaggtctgagcattggctacgttgatttggatgtg...

Basic information

species Physcomitrella patens
transcript PP1S40_14V6.1
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|100394121|gb|BY971949.1|BY971949
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAAGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|19783627|gb|BQ040046.1|BQ040046
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|162279659|gb|FC455385.1|FC455385
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|162190540|gb|FC366178.1|FC366178
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|100359351|gb|BY965704.1|BY965704
EST:     GAGCGATGCGCTCAGGTTGTTGGCAGATGACGTCGTCGTCCAGAGGAACG                         ATTTTGTCATCTAAC
genomic: -AGCGATGCGCTCAG-TTGTTGGCAGATGACGTCGTCGTC-AGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAAC
EST: gi|162186279|gb|FC361587.1|FC361587
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|100387917|gb|BY970662.1|BY970662
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAG
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAG
EST: gi|208377701|gb|DC932237.1|DC932237
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGAAACG                         ATTTTGTCATCTAACTCTGGAGGA
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGA
EST: gi|162206261|gb|FC382331.1|FC382331
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|19790819|gb|BQ042072.1|BQ042072
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|208351656|gb|DC910044.1|DC910044
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCNTCANAGGAACG                         ATTTTGTCATCTAACTCTGG
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGG
EST: gi|100399261|gb|BY954281.1|BY954281
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|162157681|gb|FC333003.1|FC333003
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
EST: gi|162204215|gb|FC379688.1|FC379688
EST:     GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACG                         ATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT
genomic: GGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGT

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: 32 (upstream exon), 35 (downstream exon)
Score: 20

CAATGGCCGCATGATTTTGAGTTTGAGGAAGATTCAACACGAATTATGCTGGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccat ... cctttgacagATTTTGTCATCTAACTCTGGAGGATTCGTTGTAGCCGTTGAGGGTCTGCGTGGTTTCGTTCCCTTTTCCCAGATTTCAGCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGGCCGCATGATTTTGAGTTTGAGGAAGATTCAACACGAATTATGCTGGGAGCGATGCGCTCAGTTGTTGGCAGATGACGTCGTCGTCAGAGGAACGgtatgtccatttttttccccgacattcctaatcgctttccagtctttgtagggacatcaagtaagaaggtctgagcattggctacgttgatttggatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA