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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggcttcccttgtttcgtcagcgtgcctgacgtcgagcgcaaagtctcacatcattgcttggtattcgttctgacaaaacatgcgaaactctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCGCGGTCGTTTTTGGCTAAGGACTAGATCGGACAAGCGAAGATGGCAACAC

Basic information

species Physcomitrella patens
transcript PP1S84_134V6.3
intron # 1
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|100415782|gb|BY993001.1|BY993001
EST:     ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGA                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|18325297|gb|BJ157293.1|BJ157293
EST:     ATAACCAACCCCACAGATAGCGGGAAGCC-------G-                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|100452222|gb|CJ975162.1|CJ975162
EST:     AACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGA                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: AACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|18329966|gb|BJ161972.1|BJ161972
EST:     ATAACCAACCCCACAGATAGCGGGAAGCC-------G-                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|18372495|gb|BJ204097.1|BJ204097
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCC-------G-                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|100436515|gb|BY961256.1|BY961256
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGA                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|18345682|gb|BJ177725.1|BJ177725
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCC---G-GTGA                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|100384294|gb|BY969425.1|BY969425
EST:     ATAACCAACCCCACAGATAGCGGGAAGCC-------G-                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG

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: 22 (upstream exon), 30 (downstream exon)
Score: 3

CGTTCGCCCCTCTGCTTCACCCTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTGAgtacgttgct ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCGCGGTCGTTTTTGGCTAAGGACTAGATCGGACAAGCGAAGATGGCAACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctcacatcattgcttggtattcgttctgacaaaacatgcgaaactctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCGCGGTCGTTTTTGGCTAAGGACTAGATCGGACAAGCGAAGATGGCAACAC
                         ttctgac  putative branch site (score: 3)
                                aaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggcttcccttgtttcgtcagcgtgcctgacgtcgagcgcaaagtctcacatcattgcttggtattcgttctgacaaaacatgcgaaactctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCGCGGTCGTTTTTGGCTAAGGACTAGATCGGACAAGCGAAGATGGCAACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG