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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA

Basic information

species Physcomitrella patens
transcript PP1S73_28V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os07g23990.1 (Oryza sativa), 3'ss of exon 18
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaattt--actaattgagt--acttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
      |  |    |   |||||| |  ||  |       | |  ||||||| || |    ||     | | |     |||  |||||   | |   ||  | ||  |||||||||| || ||||| || || || ||||| || ||| | ||||| ||||| ||| | |||||||||||||||||||| ||||| || ||| | |   
----agtacaggtttcactgttgactacttcac-----ttaatgctttcatcatttaatgatattgcttgattatctgtttcaactaacatacttgtctgttattttagACTGCTGCGAGCTACCATGCCATAGCCATTGCTCTCTCATTGATGGAAGCTTATTCCTTGAGTGTTCAGCATGAGCAAACAACCTTGCAAATTCTTCGTG

upper sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaatttactaattgagtactt-ctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
                                                             ||   |  || |   || ||  |   | | || || || || |||||||||||||| || || ||||| || ||||| |||||  | ||||| || ||||| || |||||||||||||| || || ||| | || ||  ||||  
------------------------------------------------------------gtagt-tggcatttttaacttgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG

upper sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT1G01320.2 (Arabidopsis thaliana), 3'ss of exon 20
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
|||| || |  |  |  | |||   | ||||  ||  | || |      || |   | ||||    |         | ||| ||||||  ||       || |||||||||||||| ||||| || || ||||||||||| ||  | |||||||| |||    | |||||||||||||||||||| ||||||   ||  | | | 
gttcttt-tcccgatgctcgttttttgttttgggaacataaat------atgtaagaaacttgatttg--------attttgctaattatgt---caaatttcagACTGCTGCAAGCTACCATGCCATAGCAATTGCGCTCTCCTTGATGGAGGCATACCATTTAAGTGTTCAGCATGAGCAAACAACCTTAAGAATCCTTCGAG

upper sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtt-tcatctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
  |     |   |  |    ||    ||  |   |||| || |     |      |||    ||| |||  ||    |||| |||| |    |  |||| || |||||||||||||| ||||| || ||||| ||||| ||||| || ||||| || |||||| | || ||||| |||||||| || ||  |||||||| | ||| 
--ttcccattctatgaaggcttaggcttaat--aagtaaaatttaccatggaagctaaatgatacgctaaaac-atgaattcactactgttatgtttctttt-cagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG

upper sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 20
-----gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtttcatctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
      ||| |   ||        |   || || ||| | |    | | || |        | | | |  |  |    || ||||| |   |    || | || |  ||||| || ||||||||||| ||||| |||||||| || ||| | ||||| || ||| |  | || ||||||||||||||||| ||||| || ||| | | | 
gaggatttcatctgaatttagaagggaaaaattattttgggccacacttgtgt--------ata-tcattcctttggagctaatttccatctcttttaatgctctc-cagACAGCAGCAAGTTACCATGCAATAGCAATTGCTCTATCATTGATGGAAGCATACCCTTTGAGCGTTCAGCATGAGCAAACAACCTTGCAAATTCTCCGAG

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), 22 (downstream exon)
Score: 5

CATGATGGAAGAGGGTCTAGGAAATATCCATGTGGCTCTTCGTTATTTACATGAGGCTCTGAAGTGCAATCAGCGGCTTCTGGGAGCTGACCACATTCAGgttcgttgta ... tctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
                              tactaat  putative branch site (score: 5)
                                           cttctgtt  putative PPT
                         aaatttactaattga  TA-rich tract