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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA

Basic information

species Physcomitrella patens
transcript PP1S39_352V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g47340.1 (Oryza sativa), 3'ss of exon 2
----gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgct-tgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
     | |      || || || || ||        | |||  |  |  |||| || | | | || |||  |  | || | | | || |    | |  |||||||||| |||||||| || |||||  | ||||| || ||| | || || |||||||||||||||||||| |||||||| || ||||| |||||  | || || 
tgtattttgtctatcaataagtttgtgtgtgaggatgctgtcaaa-tgctttcaatcaagttctgtaaggctgtaacagg-gttttgtgc---tctgctttgcagTGAGATTGCCAAGCACTTGTCACTTCCACCAGTAAAGCTCCATTGTAGCATGCTTGCTGAGGATGCAATTAAAGCTGCCGTGAAAGACTATGAAGCAAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G064336_T01 (Zea mays), 3'ss of exon 2
------gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
      ||    | |   |  |   || |   ||| |||    |  |  | |  || ||| ||   |||    |  | |  |||| | | ||   | ||||| |||||| ||||| || || |||||  | ||||| || ||| | || |||||||||||||| |||||||| |||||||| |||||||| |||||| | || || 
gccactgttgttaggatttggttcttgtgatttttctggacactatcagaat--ccttta-gc---aaactccactgtaactggttttgttaccctgtttttccagTGAGATTGCAAAGCACTTGTCCCTTCCACCAGTAAAGCTCCATTGCAGCATGCTTGCGGAGGATGCCATTAAAGCTGCTGTGAAAGACTACGAAGCCAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G868273_T02 (Zea mays), 3'ss of exon 2
---------gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
          | |  | ||  |  |   ||||   ||| ||||   |  |  | |  |  ||| ||    |  | |  | | ||| ||||      |  | |||| ||| || || || || || |||||  | ||||| || ||| | || |||||||||||||| |||||||| |||||||| ||||| || |||||| | || || 
cctcgctgtatttttagggtttggttgttgagatttttctgggcactatcagaatccc--tta-gcaaagaccactgtaacttgttgtgt------tactcttttccagGGAGATCGCGAAGCACTTGTCCCTTCCACCAGTAAAGCTCCATTGCAGCATGCTTGCCGAGGATGCGATTAAAGCTGCTGTAAAAGACTACGAAGCCAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G141252_T01 (Zea mays), 3'ss of exon 2
----gtgtacaag-gcattatgtgtgagtactttatgggtgttgacctattttccattatgct--tgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
    || |  ||  |   |   | ||        |||  |       |  ||    || |  |  ||| |  |  |   |   |   |     | | |||||||||| || ||||| || ||  ||||| | ||||| |||||| |||||||||||||||| |||||||| || || || || || |||||||| ||| |||| || 
gtaagtttcgaatcggcctggatatggtcgtcccatgcattccatatttcttggggttgttgtactgatacgtctatatacacgcctttccattgtcttttttgcagCGAGATTGCGAAGCACCTGTCTCTTCCACCAGTGAAGCTGCACTGCAGCATGCTCGCTGAGGACGCAATCAAGGCCGCCGTGAAGGATTACGAGGCAAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G19310.1 (Glycine max), 3'ss of exon 2
gtgtacaaggcattat-gtg-tgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
 | ||    |  |  |  || | | |  ||||||  |  |  | | || ||  |  |  ||     || ||   | |||         ||  | ||||||||||| ||||| || ||| | ||  | ||||| || ||| | ||||||||||||||||||||||||||||| ||||| ||||| || || ||  | ||||| 
-tctagggagtttagtcatgctaaatgttttatgattaatcgcat-ttgtctctggttattagtctatgaattgaagtgacacataatttaatgttttgcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G21010.1 (Glycine max), 3'ss of exon 2
---------gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
          ||   ||||  ||||   | |  || ||    || |  |||| |       |  | ||   |  | ||   |       ||  | |||||      |||||| ||||| || ||| | ||  | ||||| || ||| | ||||||||||||||||||||||||||||| ||||| ||||| || || ||  | ||||| 
agcttagtcatgctaaaggttttattattaatcacattt---gtctccacctctccggttattagtttatgaattgaagtgacacataatgaatgttttt------cagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTCAAGCTTCACTGCAGCATGCTTGCTGAGGATGCTATAAAAGCAGCTGTTAAAGATTATGAAGCTAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G09670.2 (Glycine max), 3'ss of exon 2
gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA------------------------------------------------
                                              |||   | || |    ||||       ||     |  | | | |  |   ||||||| ||||| || ||| | ||  | ||||| || ||| | |||||||||||||||||||| |||||||| |||||||| || || |||||  | |||||                                                 
---------------------------------------------gttctggtttgttgttgagatcttgatgtggcaaataagcaatgtcct---gcagtgaaattgcaaagcatctttcacttccaccagttaagctccactgcagCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAGCGTGCTAAGGCAACTGCTAGCGGAGAGGCAGCAACAGAAGAGAAGCCT

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA17G09670.1 (Glycine max), 3'ss of exon 2
----gtgtacaaggcattat-gtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
     ||   ||    |||| || |  ||  |   |   || ||     || |   || |  |||| |  || | |  ||     |  | | | |  |   ||||||| ||||| || ||| | ||  | ||||| || ||| | |||||||||||||||||||| |||||||| |||||||| || || |||||  | ||||| 
catcatggcaaaatagttatagttttggttatgctttcatgatggatagttctggtttgttgttgagatcttgatg--tggcaaataagcaatgtcct---gcagTGAAATTGCAAAGCATCTTTCACTTCCACCAGTTAAGCTCCACTGCAGCATGCTTGCTGAAGATGCTATCAAAGCGGCCGTTAAAGACTATGAAGCTAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv01s0127g00460.t01 (Vitis vinifera), 3'ss of exon 1
-gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttt--tgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
    | ||    ||| | | |   | ||       | | ||  | |||    |||   ||      ||    |   || ||||  |||||  |     || || || |||||||||||| | ||| | || || |||||| |||||||||||||||||||||||||||| ||||| || ||||| || || ||  | || || 
aacttgcattatattttttattgttgctactgatttctcgaagtttttatttttaatttttgtctttttgttc---tgatgtgtatatttgatgacaatgaagGGAGATTGCCAAACATCTCTCTCTTCCTCCAGTGAAGCTGCACTGCAGCATGCTTGCTGAGGATGCAATTAAGGCAGCTGTCAAAGATTATGAAGCCAAG

upper sequence: PP1S39_352V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ10697 (Selaginella moellendorffii), 3'ss of exon 2
gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
                                |    |   ||  ||   |  ||   |   ||  |||    | |  | |      || || || ||||||| || ||||| ||| ||||  |||| || |||||| | ||||||||||||||||| |||||||| || ||||| ||  | || || ||| | || || 
--------------------------------gtaacttttcttcttgagaggatttctccgaggctaagctctctcctct------ttcttcttcgcagTGACATCGCCAAGCATCTGTCGCTGCCGCCAGTGAAGCTCCACTGCAGCATGCTTGCCGAGGATGCGATCAAAGCCGCGATCAAAGATTACGACGCGAAG

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|162273916|gb|FC450055.1|FC450055
EST:     GCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|18330965|gb|BJ162971.1|BJ162971
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162269290|gb|FC445821.1|FC445821
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162272889|gb|FC448838.1|FC448838
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|208388839|gb|DC945415.1|DC945415
EST:     CTATGGAGG-AGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: CTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|18339607|gb|BJ171634.1|BJ171634
EST:     GTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162240736|gb|FC417459.1|FC417459
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|100445500|gb|CJ975649.1|CJ975649
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162232570|gb|FC408913.1|FC408913
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|67573048|gb|BJ945872.1|BJ945872
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162269289|gb|FC445820.1|FC445820
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|67696431|gb|BJ956664.1|BJ956664
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162240735|gb|FC417458.1|FC417458
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|37840506|gb|BJ598514.1|BJ598514
EST:     TGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: TGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|100446443|gb|CJ970742.1|CJ970742
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162272888|gb|FC448837.1|FC448837
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
EST: gi|162236414|gb|FC412781.1|FC412781
EST:     GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAG                         TGATATTGCCAAACATTNGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT
genomic: GAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCAT

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: 82

CTTCTGAGTGGATCAAGGGGAAGCCTATGGAGGAAGCCGTGAGTATCAGAAACAGgtcagcaact ... ttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA
                                       tattttttttttgc  CT-rich tract
                                       tattttttttttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtacaaggcattatgtgtgagtactttatgggtgttgacctattttccattatgcttgaaagattaaagcatgtggtgtgggtattttttttttgcagTGATATTGCCAAACATTTGTCTTTGCCACCTGTGAAGTTGCACTGCAGCATGCTTGCTGAGGATGCTATTAAAGCGGCTGTGAAGGACTACAAGGCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG