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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_153V6.2
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






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctttctggttcacacaggcaagttctcagttgacttgtaatgatgctgcagAGCATAACGGAGTATGAAGAGCATGAAAAGAGGGCATGGAGTGTGGATTTTTCACGAACTGATCCCACTATGTTAGTCTCGGGAAGCGATGATGGCAAG
                               agttgac  putative branch site (score: 4)
                                      ttgtaat  TA-rich tract