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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttctcagagatcaagaatatgatgaaaagaaattagggggaggtcacggttatttagctaattgtcttgtgcatctttgacgctttgtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAGTCGGATTCTTCCAAAGTGAGTCTTAGATCATGCGCCATCAAGGAGAGGT

Basic information

species Physcomitrella patens
transcript PP1S93_184V6.2
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|100439582|gb|BY962005.1|BY962005
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100410653|gb|BY992203.1|BY992203
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100418577|gb|BY957487.1|BY957487
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100386759|gb|BY970300.1|BY970300
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100396738|gb|BY953802.1|BY953802
EST:     GCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATA-TTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100414275|gb|BY992697.1|BY992697
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100383704|gb|BY969233.1|BY969233
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100392765|gb|BY971873.1|BY971873
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100363317|gb|BY984465.1|BY984465
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100446522|gb|CJ970821.1|CJ970821
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|162190451|gb|FC365673.1|FC365673
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100448350|gb|CJ972649.1|CJ972649
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100449378|gb|CJ973677.1|CJ973677
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|208380676|gb|DC903238.1|DC903238
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100385661|gb|BY987726.1|BY987726
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|18365985|gb|BJ198063.1|BJ198063
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100421943|gb|BY957792.1|BY957792
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|18373493|gb|BJ205071.1|BJ205071
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100398897|gb|BY990570.1|BY990570
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100369066|gb|BY985005.1|BY985005
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100439903|gb|BY980297.1|BY980297
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100411897|gb|BY992394.1|BY992394
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|208347528|gb|DC913166.1|DC913166
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|100431307|gb|BY978461.1|BY978461
EST:     GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
EST: gi|67578528|gb|BJ950695.1|BJ950695
EST:     GCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATANNNNNNNNNCCAG                         TTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG
genomic: GCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATA-TTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAG

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: 33 (upstream exon), 33 (downstream exon)
Score: 7

GAGCTGGATTGGGTGCAGCAGACCCAAGGCTTCGTGTATCACTTGCGCAAGGCTGTAAAGATAGTTGACTTACTCGGCGGCATCGATATTTTTTTTCCAGgttacatcct ... gtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAGTCGGATTCTTCCAAAGTGAGTCTTAGATCATGCGCCATCAAGGAGAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcacggttatttagctaattgtcttgtgcatctttgacgctttgtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAGTCGGATTCTTCCAAAGTGAGTCTTAGATCATGCGCCATCAAGGAGAGGT
        ttatttagctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttctcagagatcaagaatatgatgaaaagaaattagggggaggtcacggttatttagctaattgtcttgtgcatctttgacgctttgtatgcgcagTTTGTTTAATGTCCCTACGCGGTCGAGATGGCGATTGTAGCACTGTTTTAGTCGGATTCTTCCAAAGTGAGTCTTAGATCATGCGCCATCAAGGAGAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG