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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtatcatctcacaaattgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatactgagctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA

Basic information

species Physcomitrella patens
transcript PP1S5_359V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G04740.1 (Glycine max), 3'ss of exon 1
tagtatcatct-cacaaat-tgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatactga-gctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
 | ||| || | ||| | | | |    ||    |||| ||||  |  | | | |  ||     |  || ||| | ||||  |    ||   | |||  | |||  || || |  || || ||||  |||||||||||||| |||||||||||  |||||||||| ||||| || ||||| ||||| || || |||||||||||
aaatattatatgcactattattactcaagaagataaaatatc--atgttatgttagaggctagagttagtgatggtttgtttgttgtggtttcttttat-cagCTAAGGCCACCTTTGGGGAGAAAGAATGGTATTTCTTCAGTCCTAGAGACCGAAAGTACCCAAATGGTGCAAGGCCAAACAGGGCAGCTGCTTCAGGGTA

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G26740.1 (Glycine max), 3'ss of exon 1
-tagtat-catctcacaaattgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatactgagctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
 | || | ||    |  | ||  |     |   |   || |      |   |  | |  || || ||       |||  ||    |||  |  || |  |||  || ||    || || ||||  || ||||| ||||| |||||||||||  | |||||||| |||||||| ||||| ||||| || || |||||||||||
ttcgtgtgcactagaagagttttaattttcttttcttctttttt-tgtggtgtgtgatgtggaagattgatgtttttttgtttgttgtggttctt-caacagCTAAGGCCGCGTTTGGGGAGAAAGAGTGGTACTTCTTCAGTCCTAGAGACCGGAAGTACCCAAATGGAGCGAGGCCAAACAGGGCAGCAGCTTCAGGGTA

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA02G07700.1 (Glycine max), 3'ss of exon 1
tagtatcatctcacaaattgaaggcagcgcc-taaactatccaacataacgattcagttgtaaaatactgag--ctttgagtaaaatgt-catg--tttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
      ||    |  | ||  |     |    |   ||        ||  || |  | |||  || | |||    |||  ||    ||| | ||  | | |  |||  || ||    || || ||||  || ||||| ||||| |||||||||||  | |||||||| |||||||| ||||| ||||| || || |||||||||||
------cactagaagagttttaattttcttaattttcttctttttgtatggagtgtgatgtggaagattgatgtttttttgtttggtgtacgtggatcttcaacagCTAAGGCCGAGTTTGGGGAGAAAGAGTGGTACTTCTTCAGTCCTAGAGACCGGAAGTACCCAAATGGAGCAAGGCCAAACAGGGCAGCAGCTTCAGGGTA

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G35630.1 (Glycine max), 3'ss of exon 1
tagtatcatctcacaaattgaaggcagcgcctaaactatccaacat-aacgattcagttgtaaaatactgagc-----tttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
    | |        ||| |  | |      |||| |    ||||| || | |   ||  || |   |  | |     | | | |||  |  ||||     |||||  ||| ||   || ||||| |  |||||||||||||||||||| ||||| || |||||||| ||||| |  ||||| ||| ||||  | |  || |||||
----accgaaattgcaatcgcggaccctttttaaaatccttaacatgaatggtattgtattacatctcctaacacacttgttattaacttaccatgg--aatgcagATAAAACAGAATTTGGAGAAAATGAATGGTATTTCTTTAGTCCAAGAGACAGGAAGTACCCAAATGGGGTGAGGCCTAACCGAGCAACTGTGTCTGGGTA

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA10G09180.1 (Glycine max), 3'ss of exon 1
----------------------------------------------tagtatc-atctcacaaattgaaggcagcgcctaaactatccaacataacga-ttcagttgtaaaatactgagctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA-
                                               |||||  |  |       | | |     |     | | |      ||  |  || |  |   || |||| |        ||   | |||| ||     || | |||||  | || || |||   || ||||||||||||| |||||||||||| ||||| || |||||||  ||||| || |||||  |  |||| || || 
gtgttagcaattgcattgttttagtttgtgtttcattcttttcttgaagtatttacttagtgggataaggcttttgttgttattgttgtttctattgtcttgaagtagtaattactaaagcaatgatagcttttcattttga--acaagCAAAGCTTTGTTTGGGGAGGATGAGTGGTATTTCTTTACTCCTAGAGATAGGAAGTATCCCAATGGAGTGAGGCCTAATAGAGCAACTACTTCTGGTTAT

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G29360.1 (Glycine max), 3'ss of exon 1
--tagtatcatctcacaaattgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatactgagctttgagtaaaatgtcatgtttgc-----tgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
  | ||    |  ||   | |    |      ||||    |     |     || ||||||  ||| |   | ||||   ||   |||  |  |||      |||||  ||  |  | || ||||||   ||||||||||||||||| || ||||| || |||||||| ||||||   ||||| ||||| || || || ||||| ||
gtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttga-gtttatacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0007g07670.t01 (Vitis vinifera), 3'ss of exon 1
tagtatcatctcacaaattgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatact-------gagctttgagtaaaatgtcatgtttg---ctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
  || |  |   | | |   |   ||   | || |  ||||     ||  | | |    |||||||||        |  ||  |||    | ||   | |    ||||||| |||||  |||| || |||| ||| |||||||| || |||||||||||| | |||||||| ||||||   || ||||||||||| || || ||||| ||
--gtttgcttctatatacctacctcatt-catatataatccttatcaattaattaaaaataaaatacttgtattaaaatttgaagttggttttccgatctatgtctgcagGTAAAGCTGTTTTTGGCGAGAAGGAGTGGTATTTTTTCAGTCCTAGAGATCGCAAGTACCCCAATGGACTAAGACCCAACAGAGCTGCTGCGTCAGGCTA

upper sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0040g02110.t01 (Vitis vinifera), 3'ss of exon 1
----------------tagtatcatctcacaaattgaaggcagcgcctaaactatccaacataacg-attcagttgtaaaatactgagctttgagtaaaatgtcatgtttgct--gcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
                |  | || | |      ||        |  |     | |      |      |||| ||   ||||      ||||        | |  | |||| |   |||  |||||  | || ||| ||   ||||||||||||||||  || |||||||| ||||| || |||||||  ||||| || ||||| || |||||||| ||
gtctgtatcacaccacttttttcttttttttcttttttctttacttcccctttgttttgtgttttatgttcacttagcaaatgtcaccctttttccttttttttttttttggtaaacagCCAAAGCTTTGTTTGGACAGGATGAATGGTATTTCTTTACACCAAGAGATAGGAAGTATCCAAATGGAGTGAGGCCTAATAGAGCAGCAGCTTCAGGTTA

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), 33 (downstream exon)
Score: 11

GTTCTTCATTACCTGTGTCGGAAAGCCGAGTCTAAGGTGTTCGCGATTCCTGTTATTGCCGAAATTGACCTGTATAAGTTCGACCCTTGGGACCTTCCTGgtatgataac ... tttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacgattcagttgtaaaatactgagctttgagtaaaatgtcatgtttgctgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
 acataac  putative branch site (score: 11)
           ttgtaaaata  TA-rich tract