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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG

Basic information

species Physcomitrella patens
transcript PP1S86_153V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                                                                                   |  | ||   ||    |   | | |       ||   | | ||      |   |      |  | |  ||     |  |||  | ||  ||||  | | |||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || ||| | ||| |||| || || || |||||| |||||
----------------------------------------------------------------------------gtatttcttgctctgttccacagttcattttg-cacacttgtgttattttctgaacttggattcatgatatttatgta----ttcaatctt-ctttagAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG

upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                                                                          | || | |   |  |  |   |   | ||        || |||   |||  |||    | |  ||      ||||  ||    ||||    |||||  ||||  | | ||| |||||||||||||| ||||| ||||||||||| |||||||| || || ||  |  | ||| |||| || || || |||||| |||||
------------------------------------------------------------------------gtatccactctctattcgacagttcattctgca-----atggctgtattgtaattcaaactgaggcatatggtttctgtgta---ttgtgcc-atgct--agAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG

upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G126795_T01 (Zea mays), 3'ss of exon 9
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                                                                                    ||| ||         |   |   |   || |    |     || |  |||| || |     |      ||    | |  |||      ||||  | | ||| |||||||||||||| || || ||||||||||| |||||||| ||||| || ||  | ||| |||| || || || || ||| |||||
-------------------------------------------------------------------------------gtatccactctattttacagttcattctgcaatggccattgctgtattataattcaaactgaggcatgtggtttttgtgtattgtgacatgctagAGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAG

upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 8
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggca-agttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
               |   |||  ||| ||| |        ||| |  ||||   || |  |||| |||| || |      ||| | |       || ||||   |  |  ||  | |  | |||     | | |   |  ||  | | ||| ||  | | |        |||||||  ||| ||| |||||||||||||||||| | ||||||||||| ||||||||| |||| || ||| ||||| | || || || ||||||||  | |||
---------------gtaaatgttgaattcaaatggtcagtttgttcttgta---tcagctctttgggtatctta---attcatta-atatttttttaatgt-catgtgcttgcttaaattttctac--agattatttactcatggctatcatttttccttt--------tgcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTTGATTTTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtctgacgtgtctttctggttcacacaggca-agttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
               |   |||  ||| ||| |        ||| |  ||||   || |  |||| |||| ||    |   ||| | |       |||||     |  |  ||  | | || |  | | | || |   | |||  | | ||| || |  | |         ||||||  ||| ||| |||||||||||||||||| | ||||||||||| || |||||| |||| |||||| ||||| | || || || ||||||||  | |||
---------------gtaaatgttgaattcaaatggtcagtttgttcttgta---tcagatctttgggtatctt---cattcatta-atattgttttgattgtcatgtgcttgcttaa-gttttctacagatt-atttacgcatggctatcattttaactttg--------gcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG

upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 8
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgtgtc-tgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                                                                  ||| | |     |   |   |    | |     ||  | ||| | |||| |    | | | | |  |  | | |   | | |   |  ||  || ||         |||||  | | ||| |||||||||||||||||  ||||||||||||| ||||||||||| || || ||| | | | | || || || || |||||| | |||
------------------------------------------------------------------ggtcctttgaatgaaaaattctgggctcgccactgactatagatttgtccttgtatatatatata-tatatatatatatgctaataaatgttttttat--------cagAGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAG

upper sequence: PP1S86_153V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 8
gtttgttttcattatgctcatgccgaagtcatagatatgtcttgatgatgtaaaatccgggctttaggtacctcacccgcccatcacactcccccttgatgtgtgtaggtgt--gtctgacgtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgc-------agAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                                                 ||| ||   |    |       |||  | |   ||| || |  |     || ||   |  |||   ||||   |  |  | |  |   | |       ||   ||||   |    | ||| ||         ||||  | | ||| || || |||||||||||| | ||||||||||| ||||||||||| ||||| ||  | ||| | || || || || |||||  |||||
-------------------------------------------------gtagaaattgtatctct----tctcttctgttaatctcaattacatcatatatgcacaaatgttgatctgcattcacaattttctaacctcccaatgatttcgagtttgttcactaagattctttttcttctagAGTGTGATGGAATACGAGGAGCATGAAAAGCGAGCATGGAGTGTTGATTTTTCACGCACTGAACCTTCAATGCTCGTATCCGGCAGTGATGACTGCAAG

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|100399476|gb|BY972738.1|BY972738
EST:     GCAGTGATTATGAGGGGATTATTACTGTCTGGGACGTGAATAGGCGCCAG                         AGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTT
genomic: GCAGTGATTATGAGGGGATTATTACTGTCTGGGACGTGAATAGGCGCCAGgtttgttttc ... gatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTT




















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: 28 (upstream exon), 34 (downstream exon)
Score: 5

AAAATTGAGCTGCCTCAGCTGGAACAAATATATCAAATCACATATCGCCAGCAGTGATTATGAGGGGATTATTACTGTCTGGGACGTGAATAGGCGCCAGgtttgttttc ... gatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                               agttgac  putative branch site (score: 5)
                                      ttgtaat  TA-rich tract