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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctacttttaatccttcacatatcatgtatgattttgaccggttctgattactagaaaaaactattccggtttatagatgtgtgtgtatgtggatgttcttacactagattctgcctcttgtatattgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTG

Basic information

species Physcomitrella patens
transcript PP1S201_115V6.3
intron # 8
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|37846632|gb|BJ604640.1|BJ604640
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208385376|gb|DC956616.1|DC956616
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|22492293|gb|BU052216.1|BU052216
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37847154|gb|BJ605162.1|BJ605162
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37835612|gb|BJ593624.1|BJ593624
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|22132035|gb|BQ826945.1|BQ826945
EST:     CAAAGAAAGCCGGGACTGCCCGCCCCTCTTCAGGAGGTTTGAGTAATGAC                         GCTGGGATCTGGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: C-AAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37833789|gb|BJ591801.1|BJ591801
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208393949|gb|DC928729.1|DC928729
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37821752|gb|BJ579818.1|BJ579818
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37825580|gb|BJ583646.1|BJ583646
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208397894|gb|DC916649.1|DC916649
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208385667|gb|DC952828.1|DC952828
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATACCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208380848|gb|DC923330.1|DC923330
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208356156|gb|DC957316.1|DC957316
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|67692042|gb|BJ952275.1|BJ952275
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37853039|gb|BJ611047.1|BJ611047
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208393538|gb|DC949700.1|DC949700
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37845884|gb|BJ603892.1|BJ603892
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|67725662|gb|BJ975921.1|BJ975921
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGCCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208381758|gb|DC928421.1|DC928421
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|37840656|gb|BJ598664.1|BJ598664
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208354258|gb|DC957450.1|DC957450
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
EST: gi|208348693|gb|DC926368.1|DC926368
EST:     ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGAC                         GCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC
genomic: ACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCC

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: 24 (upstream exon), 35 (downstream exon)
Score: 11

TGAAGATTATGATGGCGGTCGTGATGTGGACGCATTTGTGACTTTCTTGAACAAGAAAGCCGGGACTGCCCGCACCTCTTCAGGAGGCTTGAGTAATGACgtatgtctac ... ttgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgtatgtggatgttcttacactagattctgcctcttgtatattgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTG
                ttcttac  putative branch site (score: 11)
                                      ttgtatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctacttttaatccttcacatatcatgtatgattttgaccggttctgattactagaaaaaactattccggtttatagatgtgtgtgtatgtggatgttcttacactagattctgcctcttgtatattgcttgcagGCTGGGATCTTGTCAGCCTTTGATGATATCCTTACCGAATTTTTCTCCGCCAAACCCGAGGAGCGTAGCGGTATTCTTTCTAAGGGAGAGGAAACAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG