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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttgtaacttgtctgattcatcgctggtgtgtgcacatgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA

Basic information

species Physcomitrella patens
transcript PP1S168_28V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G00610.1 (Glycine max), 3'ss of exon 3
tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttgtaacttgtct-gattcatcgctggtgtgtgcacatgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA
  || || | |        ||    |||    ||||||||| |  ||| | |     |    | ||| ||||    |  | | ||         ||   ||||| ||  ||||||| |||||||| ||| | |||||||| || ||||||||||| || |||||||| || || || || |||||||  ||||| ||||||
-tattatttcaacatttcatgttacttactaatcattaatgtatggacataaaacattgttatatcttgattttatggggttttggttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G23780.1 (Glycine max), 3'ss of exon 3
--tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttgtaacttgtctgat-tcatcgct-ggtgtgtgcacatgat-gcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA
  |  |||||  | | |    ||    | |||| |  ||| ||   |||  | ||   |  ||   |   || | |||  | ||| || |    || | |   ||||| ||  ||||||| |||||||| ||| | |||||||| || ||||||||||| || |||||||| || || || || |||||||  ||||| ||||||
cgtactaatc--attaatgtgtggacataaaacattgtta-tgtcatgattttatg--gggacccattccatataatcatttggtttgcgttgttgtttgtttagATCGGCATTGGAAGGGGATTGTGGATTCCTTGCTGCAAACCTTTATGCTAAGAGTGTTTTTGGGGAAGATGCTTTGGTGAATGTGAGCATTGAAAAGCAA

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 3
tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttg--taacttgtctgattcatcgctggtg-----tgtgcacatgatgcg---cagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA
           |||||| | |  |   ||    ||| | |||     |||  | ||   |||     |  ||||||   |  |      |||   |  | || |   ||| || ||  |||| ||||||||||| ||||||||||| || || ||||| |||||||| ||||||||||| || || || ||  | |  |||||||| || 
--------ggggtgaaattcgtgtccaaa--cacatcactgcttcttccttgtcttacctaatacaacccattcatttttcattctccttgttggctggttgggtttcagGTCAGCACTGGATGGTGATTGTGGATTCTTGGCTGCTAACCTCTATGCAAAGAGCGTGTTTGGGGAGGATGCCTTGGTAAACATAAGCATTGAGAAACAG

upper sequence: PP1S168_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0018g02080.t01 (Vitis vinifera), 3'ss of exon 3
--tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttgtaacttgtctgattcatcgctggtgtgtgcacatgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA
    ||| | ||  |   |  |   ||   ||   | ||  |      | ||||||    |  ||   |   |  || |   | | |     |    |  || || ||  | || || || ||||| ||| | || ||||| ||||| || |||||||||||||| ||||| || ||||| |||||||  |||||||| |||
accaatagtttaccttctatcttagttcccaagggccttgtttt--ccaactgattaatcattttactttgcttgtcaccattctttcttggttggacatagCTCGGCATTAGATGGGGAGTGTGGGTTCCTTGCAGCAAACCTATACGCAAAGAGCGTATTTGGAGAGGATGCTTTAGTAAATGTGAGCATTGAGAAACAA

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|162168142|gb|FC343832.1|FC343832
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37847066|gb|BJ605074.1|BJ605074
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATNTATATGNTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37837708|gb|BJ595716.1|BJ595716
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37850559|gb|BJ608567.1|BJ608567
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|162174369|gb|FC350440.1|FC350440
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37842166|gb|BJ600174.1|BJ600174
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37827266|gb|BJ585278.1|BJ585278
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|18338077|gb|BJ170101.1|BJ170101
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37845300|gb|BJ603308.1|BJ603308
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|37827044|gb|BJ585056.1|BJ585056
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
EST: gi|162167676|gb|FC343990.1|FC343990
EST:     TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACC                         ATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA
genomic: TTCTTGCAGCATATTGTGGATTCCACCAACATGAAGTGTCTCACTCCACCgtaagtaatc ... tgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctgattttgtaacttgtctgattcatcgctggtgtgtgcacatgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA
      attttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcataatctaagtgaaaattgccttttaaacttcattaatgcagtgacctgattttgtaacttgtctgattcatcgctggtgtgtgcacatgatgcgcagATCTGCTATGGAAGGTGATTGTGGCTTCTTGGCTGCAAATCTATATGCTAAGAGCGTATTTGGGGAGGACGCATTAGTTAATGTGAATATTGAGAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA