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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttcttcactaactgtgagttgtcatgttcatgttccttggtgcccattagcctgcaggtgtggcattaatttggataattgatacttgataactgatagctcttagtatttgtttaattcatgtctttgttttacaaaaccccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTACAAGAGGGCTGGGAGATGGAAACAGTCGGTCGCTCTTTCTAAGAAGGATA

Basic information

species Physcomitrella patens
transcript PP1S452_30V6.1
intron # 26
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|162243866|gb|FC423183.1|FC423183
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATTTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
EST: gi|162195289|gb|FC369276.1|FC369276
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATTTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
EST: gi|162150854|gb|FC327334.1|FC327334
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATTTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
EST: gi|162227861|gb|FC403669.1|FC403669
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATTTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
EST: gi|162172579|gb|FC348624.1|FC348624
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATTTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
EST: gi|162271744|gb|FC448877.1|FC448877
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
EST: gi|162211494|gb|FC387366.1|FC387366
EST:     AGTCCATTGATATGTATGATAACTTTGATCAGATTTCAATGGCACAGCGG                         ATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC
genomic: AGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTAC

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), 32 (downstream exon)
Score: 13

GGCTCTCAATGGCTTATACATTGAAGATGAGGATTACGAACGACTCAGAGAGTCCATTGATATGTATGATAACTTTGATCAGATGTCAATGGCACAGCGGgtaattcttc ... accccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTACAAGAGGGCTGGGAGATGGAAACAGTCGGTCGCTCTTTCTAAGAAGGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagctcttagtatttgtttaattcatgtctttgttttacaaaaccccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTACAAGAGGGCTGGGAGATGGAAACAGTCGGTCGCTCTTTCTAAGAAGGATA
                  gtttaat  putative branch site (score: 13)
                                              ccccttc  putative PPT
         ttagtatttgtttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcttcttcactaactgtgagttgtcatgttcatgttccttggtgcccattagcctgcaggtgtggcattaatttggataattgatacttgataactgatagctcttagtatttgtttaattcatgtctttgttttacaaaaccccttcagATTGAGAAGCACGAACTTCTGGAAATGCGACGAGTTGCAGCTTACGTCTACAAGAGGGCTGGGAGATGGAAACAGTCGGTCGCTCTTTCTAAGAAGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG