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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgttttgcaatgacgtttagaaaaagtgaccagaagtgtcagcgacattttacaagttggctttctttaacctgtttgtggtttatatcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTATCAGAGAAGAACTTGCGGGGTTTGATCGAGTTCTGTATCAGGGAAAGAG

Basic information

species Physcomitrella patens
transcript PP1S64_220V6.1
intron # 6
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|162155391|gb|FC332005.1|FC332005
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162181882|gb|FC357689.1|FC357689
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAAT
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAAT
EST: gi|100352692|gb|BY945399.1|BY945399
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAGGGGAATA-CT                         CCCCGAGGATTG
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTG
EST: gi|162171669|gb|FC348130.1|FC348130
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAAT
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAAT
EST: gi|162199479|gb|FC373781.1|FC373781
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162223962|gb|FC400320.1|FC400320
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162160782|gb|FC336681.1|FC336681
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|100399005|gb|BY990625.1|BY990625
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGGATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162197024|gb|FC373364.1|FC373364
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGGATCCCACTGGTCAATG
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATG
EST: gi|162252058|gb|FC428297.1|FC428297
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162156210|gb|FC332585.1|FC332585
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|100444613|gb|BY982442.1|BY982442
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTTGGTTTT-ATCAATCCAGGGAATCCCACTGGTCAATGTCT
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATT-GGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCT
EST: gi|162153784|gb|FC329915.1|FC329915
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162154422|gb|FC330424.1|FC330424
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATC
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATC
EST: gi|100356462|gb|BY946377.1|BY946377
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGGATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGG-AATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|100364771|gb|BY947900.1|BY947900
EST:     CAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGGAGGGAAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGGAATCC-ACTGGTCAATGTC
genomic: CAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAA-TAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGG-AATCCCACTGGTCAATGTC
EST: gi|162166622|gb|FC343514.1|FC343514
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162191243|gb|FC367921.1|FC367921
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162170441|gb|FC347626.1|FC347626
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|100388497|gb|BY952099.1|BY952099
EST:     AAGGG-TTGGGAGAAATCTGTAAATGAAGCTCGCAGGGAAGGGA-TAACT                         CCCCGAGGATGGGTTTTTATCAATCCAGG-AATCCCACTGGTCAATGTCTA
genomic: AAGGGGTTGG-AGAAATCTGTAAATGAAGCTCGCAGG-AAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162191349|gb|FC368145.1|FC368145
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162246304|gb|FC421049.1|FC421049
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162152416|gb|FC327979.1|FC327979
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGGATCCCACTGGTNCA-TGTCT
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGT-CAATGTCT
EST: gi|100446806|gb|CJ971105.1|CJ971105
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCC-ACTGGTCANTGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162187053|gb|FC362835.1|FC362835
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162244637|gb|FC424604.1|FC424604
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
EST: gi|162189527|gb|FC365749.1|FC365749
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTT
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTT
EST: gi|100388392|gb|BY951994.1|BY951994
EST:     TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACT                         CCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA
genomic: TCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTA

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), 35 (downstream exon)
Score: 84

CACATTGGTGCCTTACTATTTGACTGAAGAAGACAACTGGGGTATGGATATCAAGGGGTTGGAGAAATCTGTAAATGAAGCTCGCAGGAAGGGAATAACTgtaagttgtc ... tcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTATCAGAGAAGAACTTGCGGGGTTTGATCGAGTTCTGTATCAGGGAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacattttacaagttggctttctttaacctgtttgtggtttatatcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTATCAGAGAAGAACTTGCGGGGTTTGATCGAGTTCTGTATCAGGGAAAGAG
                      ctttaac  putative branch site (score: 84)
                                       tttatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgttttgcaatgacgtttagaaaaagtgaccagaagtgtcagcgacattttacaagttggctttctttaacctgtttgtggtttatatcatgttcagCCCCGAGGATTGGTTTTTATCAATCCAGGGAATCCCACTGGTCAATGTCTATCAGAGAAGAACTTGCGGGGTTTGATCGAGTTCTGTATCAGGGAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC