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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG

Basic information

species Physcomitrella patens
transcript PP1S352_68V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 6
gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatg-acagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG
                                  || |||  | ||||| | |   |||||  |        |  |  |  | || |    |  |   || | || ||  ||| | | |  |  | ||     | ||||  ||   |||||||||||| | |    ||||||||||||||| ||  ||||||| |||||||| || || || ||||| || || |||||  ||||||||||||| || |
----------------------------------ttctgatctgttaccccctt--atattata--------tatatattaaaattactcattgtccctcac-tcatat-gaactcatggattatgatc---aaacattatatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 11
gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatg-acagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG
                                            | ||| | |      ||  |  | || | | |       |     |||  |   || | |||||  ||| | | || |  | ||     | ||| | ||   |||||||||||| | |    ||||||||||||||| ||  ||||||| |||||||| || || || ||||| || || |||||  ||||||||||||| || |
--------------------------------------------tcaccccctttccccttatattatttatataataaaattactgcttgttgtccttcac-tcgtat-gaactcatgtattatgata---aaacatattatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 4
gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG
                                     |  |||  |      |  |||    | | ||   |         || | |||   || | |    || || |||   |  |||||   |     |   || ||  || |||||||||||| | | |  ||||||||||||||||||  ||||||| ||||||||||| || || || || || || ||||| ||||| ||||| || || |
-------------------------------------tatggtggtg--atctgaaatccaaccacagaaata------aaagcttagcaaaaaaaaaaaaaattgt-cagttttccagtttgacagaga-tatccactttttg-cagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTAGTTTTAAGGCTAACACAAAGGCCCTAGCCGAAAATGAAGGGG

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 11
gtgatggtttgggtca-ctgcttacaattc--tatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatca--gctgtaatagatcgcatcgtacagaag------tgaagtttcttaatttctgagcatttca--tgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG
  |    |||   ||| |   ||| |   |   || ||  |  |   |||   ||| |   | |      ||||  |  | || | ||    ||| |   || | |       | |  |      | || | | ||  |  ||||  ||   |  | ||||||||||||| | |    ||||||||||||||||||  ||||||| ||||| ||||| ||||| || || || || ||||| ||||| ||||| || || |
--gtaaatttaaatcatccaattatatgccacaatgttaatatgagattagttcttggtggaataggtttgtttcct-gcatgcaaattgatgctctggcagctagttctactctgtgggttctctaaactctgtttttaactgaatataaaaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 11
gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG
                                           ||       | |      ||   | |     |||    | |  ||||     | |    |||       |||     |     || ||    || ||  || |||||||||||| | | |  ||||||||||||||||||  ||||||| |||||||||||  | || || || || || ||||  ||||| ||||| || || |
-------------------------------------------ttagtaatatggtggtgatctgaaatccaaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagagatctc----cactttttg-cagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG

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|162191185|gb|FC367863.1|FC367863
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|37832281|gb|BJ590293.1|BJ590293
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|162246422|gb|FC421089.1|FC421089
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|162183079|gb|FC360645.1|FC360645
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|162186605|gb|FC363577.1|FC363577
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|162191186|gb|FC367864.1|FC367864
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|162166471|gb|FC343168.1|FC343168
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|162186604|gb|FC363576.1|FC363576
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|208368657|gb|DC947932.1|DC947932
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
EST: gi|67700043|gb|BJ960276.1|BJ960276
EST:     CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAG                         CCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC
genomic: CAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCC

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: 22 (upstream exon), 35 (downstream exon)
Score: 4

CATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTCCAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGAGgtgatggttt ... ttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG
                            tcttaat  putative branch site (score: 4)
                       aagtttcttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatggtttgggtcactgcttacaattctatatttgtgaggttttaccgcttagaatatttcaagagttttttcacgtggagatcagctgtaatagatcgcatcgtacagaagtgaagtttcttaatttctgagcatttcatgacagCCTCAAGCACGAGCACTAGCTGAAAAGGAGGGATTCAAAGTAAGCGTTGCCAAGACCAGCTTCAAAGCCAATACCAAGGCACTAGCTGAAAACGAGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA