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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttagtcatctcttcgtagatcgttgaaagccatctgaagttccaatattgatgttcgattttgcatgcttgtaaactcgcagtgcatcctggtagatctcattattctgacctttgttactgttttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG

Basic information

species Physcomitrella patens
transcript PP1S71_187V6.1
intron # 5
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|67694755|gb|BJ954988.1|BJ954988
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|67575491|gb|BJ948315.1|BJ948315
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|162171775|gb|FC348951.1|FC348951
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|162219672|gb|FC395876.1|FC395876
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|67698963|gb|BJ959196.1|BJ959196
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|15590673|gb|BI675289.1|BI675289
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|162184261|gb|FC359683.1|FC359683
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAAGGCA-GCC
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGA-GGCAAGCC
EST: gi|208381504|gb|DC919506.1|DC919506
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|162202798|gb|FC379780.1|FC379780
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|16137490|gb|BI894354.1|BI894354
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAANAGCCAAAACCNTGGTGTGANA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
EST: gi|18339257|gb|BJ171284.1|BJ171284
EST:     CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAA                         GTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA
genomic: CTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCA

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: 26 (upstream exon), 30 (downstream exon)
Score: 7

CACGGCTGGTAAGGTTGATATTCTCGTTGCTGGTATTGGTACTGGCGGAACTGTAACTGGAGCCGGTCGCTTCTTGAAAAGCCAAAACCCTGGTGTGAAAgtgagtttag ... ttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgcatcctggtagatctcattattctgacctttgttactgttttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG
                                        ctgtttt  CT-rich tract
                                           ttttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttagtcatctcttcgtagatcgttgaaagccatctgaagttccaatattgatgttcgattttgcatgcttgtaaactcgcagtgcatcctggtagatctcattattctgacctttgttactgttttgattacagGTTATTGGAGTTGAGCCAACTGAGAGCAGTGTACTTTCTGGAGGCAAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG