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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcacattaattgcttattatttggcgtcagcgagctcattgtcacttctcgattcagtcataacgaactaaaggtatggcattgatgatgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG

Basic information

species Physcomitrella patens
transcript PP1S58_256V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 2
cctcacattaattgcttattatttgg-cgtcagcgagctcattgtcacttctcgattcagtcataa--cgaactaaaggtatggcattgatgatgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG
    |   ||| ||||||   ||  |   | | | |  |   |  || ||        |  ||| |   || |       ||     |  |  |  ||  ||||||||||| || ||||| ||||| |||||||| ||||||||||| || |||||  | |||||||| || ||  | ||  | |   | |||| ||||||||
---aaatctaactgcttagagttaagattttatctatttgtcttgcaattggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 2
cctcacattaattgcttattatttggcgtcagcgagct--cattgtcacttctcgattcagtcataacgaactaaaggtatggcattgatgatg-atatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG
  |  |  ||   | ||| | |  |  || | | |  |     ||| |     |     ||   |      ||     ||  |   |||| ||   | ||||||| || || || |||||||| ||||||||||| ||||||||||| || |||||  | |||||||| || ||  | ||  | ||  | |||| ||| ||||
--tatcgataggagtttagt-tcagatgttatctaattgtttctgtaaaagggcacaaaaggtgttgttgtctgttattaatgagctgattatatgtttgcagGCCGTAACAGCTATGGTGCAACAAGCTATGCAATATATTGATGAGACACCAGATATCGAAACTCGCATAGAACTCATCAAAACGTTGAACAGTGTGTCTG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------cctcacattaa--ttgcttattatttggcgt------cagcgagctc--attgtcacttctcgattcagtcat-aacgaactaaaggtatggcattgatga-------tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG
                                              |  ||||  ||    |||| ||||          |  ||| ||  | | | |||     ||| | | |  |||  | | |     ||  | || | |       |||| ||||||||||     | |||||||| ||||| ||||||||||||||| | || | |||| |||||||||| |||||| | ||| ||||||| |||| |||| |||
gtcacactactttctatcgatttagcttttgaaacctgcttgtggtagtttaaggttttcgattacttggaacggtttctactgagttctgaatcttactgagaaattgaatgaagaactgagtgagatattgaaagtggttaggtctcttgatttgcagGCTGTACAATCCATGGTGCAACAAGCAATGCAGTATATTGATCAGACACTAGACATAGAAACTCGGATTGAGCTTATTAAGACTCTAAACAATGTAGCTG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G09900.1 (Arabidopsis thaliana), 3'ss of exon 2
--cctcacattaattgcttattatttggcgtcagcgagctcattgtcacttctcgattcagtcataacgaactaaaggtatggcattgatgatgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG
  | |||| ||      |    | ||   || |          |   |  |    | |||  ||| ||  | |     | ||  |    |    |  |||||||||||    | |||||||||||||| ||||||||||| ||| | || |||||| | |||||||| || ||| | ||  |||| || |||| ||||||||
agcttcacctttccatgtacaaaattatagttaaaagtaaggatacaaagtgataagtcaa-catcactgattttttttttgtgaact-tctccacttgcagGCTGTGCAATCCATGGTGCAGCAAGCAATGCAGTATATCGATCAGACACCAGACATTGAAACTCGGATAGAGCTTATCAAGACGCTGAACAATGTATCTG

upper sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 2
cctcacattaattgcttattatttggcgtcagcgagctcattgtcacttctcgattcagtcataacgaactaaaggt---------atggcattgatgatgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG
      |||   ||    || ||||| || |   ||  |  || ||   ||  |||  || || |    |||  |||         ||||   |  |  |  |   |||||||| ||||| ||||| |||||||||||||||||||||||  | || || ||  | ||| ||   |||||| | ||| | || || |||| ||| ||||
-----tatttgctggccctt-tttggagtaaaaaagtgc--tgccatacctttatttggtgatcattt-ctatgggttgctatttcatggttattttatttttgcacagGCTGTAACTGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTG

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|162156858|gb|FC332804.1|FC332804
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|100438193|gb|BY961700.1|BY961700
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|208367351|gb|DC939867.1|DC939867
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|208350568|gb|DC910373.1|DC910373
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|208363544|gb|DC939749.1|DC939749
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|100418836|gb|BY975763.1|BY975763
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|100385804|gb|BY950998.1|BY950998
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|162225703|gb|FC401845.1|FC401845
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|162269559|gb|FC445115.1|FC445115
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|18344483|gb|BJ176523.1|BJ176523
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
EST: gi|100416003|gb|BY957030.1|BY957030
EST:     TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAA                         GCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA
genomic: TTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCA

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), 26 (downstream exon)
Score: 4

GGTGACTGAAATCATTCGATTGTGCTATGAAGGCAAGGCATGGAAGACCCTTAATGAGCAAATTCTGCTTCTGTCGAAGCGACGGTCACAACTTAAGCAAgtaagaggtg ... tgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttctcgattcagtcataacgaactaaaggtatggcattgatgatgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG
                      aactaaa  TA-rich tract