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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacgggtggttggtgtggatgaatctgtttcacttatggtgcaccacatgtgaggcctgttcagaagagttgcctaatgtgaacacatggtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGATACTGGCCTTCTCTATTCGCGAAGCTATGCGAGAAGAGGAGCGTCGATG

Basic information

species Physcomitrella patens
transcript PP1S49_284V6.1
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|67696799|gb|BJ957032.1|BJ957032
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|67709489|gb|BJ965305.1|BJ965305
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|162265808|gb|FC442395.1|FC442395
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|18368145|gb|BJ200230.1|BJ200230
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|18343044|gb|BJ175081.1|BJ175081
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|67720340|gb|BJ970599.1|BJ970599
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|37822193|gb|BJ580259.1|BJ580259
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|67573418|gb|BJ946242.1|BJ946242
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|18327667|gb|BJ159670.1|BJ159670
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGNGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|67701850|gb|BJ962083.1|BJ962083
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|18335904|gb|BJ167925.1|BJ167925
EST:     CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
EST: gi|162265807|gb|FC442394.1|FC442394
EST:     CCTGCACTTACGCCTGTTTCATCTTCCACGATGACGGCATTGCCATCACT                         GCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA
genomic: CCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGA

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: 30 (upstream exon), 35 (downstream exon)
Score: 10

CCGAGCTCTCCCTCGATCCCGTATCGCCACCATGTCGATCAGCGAGCTTGCCTGCACTTACGCCTGTCTCATCCTCCACGATGACGGCATTGCCATCACTgtaagcattc ... gtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGATACTGGCCTTCTCTATTCGCGAAGCTATGCGAGAAGAGGAGCGTCGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgtgaggcctgttcagaagagttgcctaatgtgaacacatggtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGATACTGGCCTTCTCTATTCGCGAAGCTATGCGAGAAGAGGAGCGTCGATG
                           gcctaat  putative branch site (score: 10)
                                              taatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacgggtggttggtgtggatgaatctgtttcacttatggtgcaccacatgtgaggcctgttcagaagagttgcctaatgtgaacacatggtaattttagGCCGACAAGATTGCAGCTTTGGTGAAGGCTGCTAACGTGTCCGTAGAGGGATACTGGCCTTCTCTATTCGCGAAGCTATGCGAGAAGAGGAGCGTCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - -tggtgca
- - - - - - - - - - - - - - - - - - - - - - -cacatgt