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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttttgtttggcaatgcatctgattacgaattggcaatgttccgaaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT

Basic information

species Physcomitrella patens
transcript PP1S263_81V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S263_81V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA04G39150.1 (Glycine max), 3'ss of exon 16
acttttgtttggcaatgcatctgattacgaattggcaatgttc-cgaaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT
                   | | | ||| |||      |  || |  || |||  || |    |||  |  |  ||| ||||| |  |   | |||  |||||||| ||||| |  ||  |    || ||    |  || ||||||||||||||||||||||||||||||||||| |||| ||| |||||||| ||  | |
------------------gtttcaatactaatattagttactctcttaactgtaatttt---ttttgcctgtttgct-acatttttttctttcttgg-cagCAATGTGTATCTTTGGTGCTTTCCCTCATTAGCAGTAGCCTGGATGCATGGCGGACACGGCAGTATGATTATTACCAGAGGGTTTTGAATGGGATATTGT

upper sequence: PP1S263_81V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA06G15820.1 (Glycine max), 3'ss of exon 16
acttttgtttggcaatgcatctgattacgaattggcaatgttc-cgaaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT
                   | | | ||| |||      |  || |  || ||| ||| |    |||  |||       ||||| |  | |  | |   |||||||| ||||| |  ||  |    || ||    |  || ||||||||||||||||||||||||||||||||||| |||| ||| ||||| || ||  | |
------------------gtttcaatactaatattagttactctcttaactgtattttt---ttttcgcctgtttgctacattttttttctctcttggcagCAATGTGTATCTTTGGTGCTTTCCCTCATTAGCAGTAGCCTGGATGCATGGCGGACACGGCAGTATGATTATTACCAGAGGGTTTTGAACGGGATATTGT

upper sequence: PP1S263_81V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA08G16620.1 (Glycine max), 3'ss of exon 17
acttttgtttggcaatgcatctgattacgaattggcaatgttccgaaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT
      ||||    ||  ||    ||||  |||   | |||  |     |||||||  |     |||     ||      ||||| |   ||| |  |||||||| || || |  ||  |    || ||    |  || |||||||| ||| ||||||||||||||||||||||||||| ||| |||||||| ||  | |
------gtttcaatattaataatgttacctattta-actgtcaca----tgtttttaggtgtgatttttaagagtgagtgttataatttttttgg--cagCAATGTGTCTCCTTGGTGCTTTCACTCATTAGCAGCAGCCTGGATGCTTGGAGGACACGGCAGTATGATTATTATCAGAGGGTTTTGAATGGAATATTAT

upper sequence: PP1S263_81V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA05G32460.1 (Glycine max), 3'ss of exon 15
acttttgtttggcaatgcatctgattacgaattggcaatgttccgaaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT
      ||||    ||  ||    ||||  |||   | |||     || ||||| || |     ||   || ||      ||||| | | |||||  |||||||| || || |  ||  |    || ||    |  || |||||||| ||| |||| |||||||||||||||||||||| ||| |||||||| ||  | |
------gtttcaatattaataatgttacctattta-actgtc----aaatgtttctgggtgtgattg--ttaag--agtgttataattctttttgg-cagCAATGTGTCTCCTTGGTGCTTTCACTCATTAGCAGTAGCCTGGATGCTTGGAGGACGCGGCAGTATGATTATTATCAGAGGGTTTTGAATGGAATATTAT

upper sequence: PP1S263_81V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv04s0044g01210.t01 (Vitis vinifera), 3'ss of exon 14
acttttgtttggcaatgcatctgattacgaattggcaatgttccgaaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT
      |||||    |  || | || |  | ||    ||   |  | ||  |||||| ||   |  || || |      ||| |  ||  || |   |||||||| ||||| |  ||  |    || |||   |  ||  | ||||||||||||||||||||||||||||||||||||| ||| || ||||| ||  | |
------gtttgatttta-attttatcatcattttagtattagctaatat-atttttgagatgatggtcattga--cagtatt-tcttgatttctag-cagCAATGTGTATCTTTGGTGCTCTCCCTGATCAGCAGCAGCTTAGATGCATGGCGGACACGGCAGTATGATTATTATCAGAGGGTTTTAAATGGGATCTTGT

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|162175952|gb|FC352358.1|FC352358
EST:     GGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAG                         CAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGG
genomic: GGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAGgtatgttttt ... ttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGG
EST: gi|162193610|gb|FC369148.1|FC369148
EST:     GGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAG                         CAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGG
genomic: GGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAGgtatgttttt ... ttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGG
EST: gi|162260564|gb|FC436152.1|FC436152
EST:     GGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAG                         CAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGG
genomic: GGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAGgtatgttttt ... ttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGG

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: 29 (upstream exon), 22 (downstream exon)
Score: 3

GATTCTGGATACCCGTGCTTTAAAGGGGGTCCGCGGACACTGCAAAATTTGCGGAAGCGTTTTCATCTAAGCTTGACAGAGGAGgtatgttttt ... ttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgtttttgtgaactttttccttcagctgacattatactgccttttgttcagCAATGCGTATCATCAGTTTTGGAGCTTATCGCTAAAAGTCTGGATGCATGGCGGACACGGCAGTATGATTATTATCAGAAGGTGTTGAATGGTATTCTTT
                           agctgac  putative branch site (score: 3)
                                           ccttttgttc  putative PPT
              aacttttt  TA-rich tract