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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA

Basic information

species Physcomitrella patens
transcript PP1S152_13V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os06g09290.1 (Oryza sativa), 3'ss of exon 6
--gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatc----------agcactagtgtgaaatctcaaaccatgtcactga-----agcaa---gtgcttgatctg-cagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
   | ||  |        || |  |     || | ||    | |  |             || |  | |  || |||      | |  || |      || |   ||| ||| |    |||| || || || ||||||||||| || ||||| || ||||| ||||| || || ||||||||||| |||||||||||||| || ||||| || || || ||
gtaagtgccgggaattcttgcatgacagaatccagtctctggctagtttctgttccatgtcatttatctttaacctccttttttttttctcacgtttggctatttgtgtttgttggaacagGGGCCGACATACGGAGTGTGTGCACGGAGGCTGGCATGTACGCCATCCGCGCTCGCAGGAAGACGGTGACAGAGAAGGATTTCTTGGACGCGGTGAATAA

upper sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 9
---gaatgatgca-ggcgactgtagaatgttgtcgaatcg---tgagttgatcagcactagtgtgaaatct----caaaccatgtcactgaagcaagtgcttgatctg------cagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
      || |    ||   | | ||||||||   |  ||    ||| |  ||         ||   | | |     | |  ||     |    ||    |||| | ||      ||||||| |||||  |||| || || ||||| || || ||||||||||||||||| |||||||| || |||||||||||||| ||| | || |||||||| ||
gtgagttgctttgtggtttcagcagaatgtttgtgtttctgcttgattcaattgatttacttgaagactttgcgatagatgatcaggttctcacatagccttgctttgttactccagGAGCGGATATAAGGAGCGTCTGCACAGAAGCCGGGATGTATGCCATTCGTGCCCGCAGGAAAACGGTGACAGAGAAGGATTTTCTCGATGCTGTCAATAA

upper sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 8
gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgat-cagcactagtgtgaaatctcaaaccatgtcactgaagcaagt-gcttgat-ctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
                       ||| ||   ||| ||||| | | | ||  || |     |      | || ||      |     | ||||| | || ||||||| |||||  |||| || || ||||| || || ||||| |||||||| || |||||||| || |||||||| ||||| ||| | || |||||||||||
----------------------gtgtggtttcatc-tgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCGCCCGCAGGAAAACGGTGACAGAAAAGGATTTTCTCGATGCTGTCAACAA

upper sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctc-aaaccatgtcactgaagcaagtgcttg-----atctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
      |       | |    || | | |   |||     ||| |      |  | |   || || | ||  ||    |     || | |||       ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||
------tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

upper sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
gaatgatgcaggc--gactgtagaatgttgtcgaat-cgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
|  || | || ||  |||  | |  |  ||    ||   |||  |  |  ||   | ||  | |  |       | | |  ||  |   |  ||| ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||
gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttca-tgctagacattggttt-tctgatagataccttttgttg-tctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA

upper sequence: PP1S152_13V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactga-----agcaagtgcttgatc----tgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
   | |   |     ||| ||       |    | ||    |   ||    | || |    | | |      ||   ||        ||  | |||  ||    | ||||||| || ||  | |||||||| || || || || |||||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||  | || |||||
--gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgttattttgggttcttggtttttctcatattctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA

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|37847976|gb|BJ605984.1|BJ605984
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         -A-----TATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|208350436|gb|DC926183.1|DC926183
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|208368723|gb|DC947956.1|DC947956
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|67720349|gb|BJ970608.1|BJ970608
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|162256307|gb|FC432317.1|FC432317
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|67579074|gb|BJ951225.1|BJ951225
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|162257096|gb|FC432556.1|FC432556
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|208366359|gb|DC947569.1|DC947569
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|162267487|gb|FC444238.1|FC444238
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|67694853|gb|BJ955086.1|BJ955086
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|67720715|gb|BJ970974.1|BJ970974
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
EST: gi|208364215|gb|DC947291.1|DC947291
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         GAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTG

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: 34 (upstream exon), 15 (downstream exon)
Score: 6

GAAAGCCGAACCCAGATTTTCAAGATCCATACGCGAACCATGAATACCGAGCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... tgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA
                                          gcttgat  putative branch site (score: 6)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatgatgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcagGAGCAGATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- -tgatgca