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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaggtcttttagttttggaagtgctcagattgatgagagcttttaacagatttcatttgacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC

Basic information

species Physcomitrella patens
transcript PP1S136_176V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 1
---tcaggtcttttagttttggaagtgctcagattgatgagagcttttaacagatttcatttgacct--cagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC
    |    |  |    || || ||||||     | | || |   ||   ||   ||   | |   |   ||||||    |   | | |   ||||    ||||| ||  | || ||||||||||||||||| |||||||||||  |||||||||| || ||||| ||||| || ||||| ||||| || |||||||| || |||
gaaccccccccctcccattgggtagtgctatagcttaggaaattattacgcaaggtt-gctaggtttgatagtgtttcttgcgtgatgtccatgga----tgcagCGTGGTGAAGATAGTGCTGCAGTTCTGCAAGGAGAACTCGCTGCAGCAGACGTTCCAGACGCTGCAGAACGAGTGCCAGGTCTCGCTCAACACCGTCGAC

upper sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 1
tcaggtcttttagttt---tggaagtgctcagattgatgagagcttttaacagatttcatttgacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC
 ||  |  || | | |    |  |     | || |      ||| || |     ||    | |||    |  || | ||     |||| ||   || | |||| ||  |||| ||||||||||||||||| |||||||| ||  |||||||||| || ||||| |||||||| ||||| ||||| |||||||||||||| |||
-catcttattgaatctatccgagaaccgcctgacttgcagtagcatt-agtgtcttaaggtcgacaaaggatttgagcgcgatgttttttttttgt-gcgcagCGTGGTTAAGATAGTGCTGCAGTTCTGCAAGGAGAATTCGCTGCAGCAGACGTTCCAGACGCTGCAAAACGAGTGCCAGGTCTCCCTCAACACTGTTGAC

upper sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------tcaggtcttttagttttggaagtgctcagattga--------tgagagctttt------aacagatttcattt--------gacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC
                                                              |||  | ||| | |||||   |   ||  |||||        | |  | | ||      || |||| |  |||         |  |  ||||       |   | |  |||    |  |||||||||| ||||| ||||| ||||| || || ||||| || ||||| |||||||||||||  ||||| || || || |||||||| || |||||||| |||
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC

upper sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
--tcaggtcttt-tagttttggaagtgctcagattgatgagagcttttaacagatttcatttgacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC
  |    | | | || | ||   |   ||     ||   |   ||||  |  | ||| || |||  | | |  | |    | |  ||| ||    |  | |||||||||||| || ||||| ||||| ||||| || || |||||||| || || ||||||||| | |||| |||||||||||| ||  | || || || |||
ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaat-ctaattttatgtatttcttca--tctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC

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|18356375|gb|BJ188434.1|BJ188434
EST:     TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGA                         TGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
genomic: TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGAgtaagtgtcc ... agttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
EST: gi|100370554|gb|BY985466.1|BY985466
EST:     TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGA                         TGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
genomic: TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGAgtaagtgtcc ... agttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
EST: gi|100416629|gb|BY975479.1|BY975479
EST:     TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGA                         TGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
genomic: TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGAgtaagtgtcc ... agttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
EST: gi|100408381|gb|BY974137.1|BY974137
EST:     TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGA                         TGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC
genomic: TTGTAGCTGTTGCACTTGGTCATGTCCACTCTCGAAATTGAAGCACGCGAgtaagtgtcc ... agttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagatttcatttgacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC
     atttcattt  TA-rich tract