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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaatatcgtcgagtttactattgatactattcatttgttgatatttttggtgttgttacctatttgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG

Basic information

species Physcomitrella patens
transcript PP1S246_34V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 3
--ttgaatatcgtcgagtttactattgatactattcatttgttgatatttttggtgttgttacctatttgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
  | || |    |  | | |   | ||   |  |  ||   || ||| |  |  || ||| |  ||| |  |      ||  ||   | || |  |  |||||||||||| || ||||| ||| ||||||| || |||||||| || || || || |||||||| |||||||||
cttagattgatttacactatgtcagtggcgcactatataatttcatactcatt-tgctgtaatttatgttttagtttgctaattcctc-ctttcataaacagCGTTTTGCTGCGGTTATCATGAGAATAAGAGAACCAAAAACTACAGCTCTGATATTTGCATCGGGTAAAATG

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 3
--ttgaatatcgtcga-gtttactattgatactattcatttgttgatatttttggtgttgttacctatt-tgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
  ||   |    || |   ||| | |  || |||  ||| | || ||  |  | |     ||| ||    |||| |   |  | ||  | |   |||    ||||||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattggtcatttatctgcagtgcttatgtctatcttttgaatctttg----cagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 3
--ttgaatatcgtcga-gtttactattgatactattcatttgttgatatttttggtgttgttacctatttgctcaacgccttgttgggcact--attgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
  ||   |    || |   ||| | |  || |||  ||| | || ||  |  | |    || |  ||| ||| |  |    |||    || |  | | | | ||||||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || |||
ttttatctgagatcaataattaatttgcatgctagacatgtctttatgctgattg----gtcatttatctgcactgc-taatgtctatcatttgaatctttgcagCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGATG

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 2
ttgaatatcgtcgagtttactattgatactattcatttgttgatatttttggtgttgttacctatttgct--caacgcct---tgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
 |   |||| |  | |  |  ||| ||  |      | | | || | |||    |  ||    |||||    ||| ||     | |  ||    | | | |  |||||||||| |||||||||||| | || ||||| |||||||| ||||| ||||||||||||||||| || || 
-ttgctatc-tgaaatcaataattaat-ttgcatgctagat-atgtctttatgctgattggtcatttgtctgcaatgctaaagtctatggtttgaatctttgtaGCGTTTTGCTGCTGTTATTATGAGGATCAGGGAACCAAAAACTACTGCACTCATTTTTGCATCTGGCAAGAT-

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|18346530|gb|BJ178575.1|BJ178575
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|100438401|gb|BY979938.1|BY979938
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|100441350|gb|BY962639.1|BY962639
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|208354942|gb|DC914206.1|DC914206
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|208376207|gb|DC910783.1|DC910783
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|208373747|gb|DC936560.1|DC936560
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|208360850|gb|DC934746.1|DC934746
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|100430149|gb|BY978271.1|BY978271
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|100410692|gb|BY992221.1|BY992221
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
EST: gi|18373885|gb|BJ205463.1|BJ205463
EST:     ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCCGAATATAACCCTAAG                         CGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC
genomic: ATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTC

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: 33 (upstream exon), 27 (downstream exon)
Score: 5

GAATATTGTCTCAACTGTTAATATGGATTGTCGCTTGGATTTAAAGAAAATTGCCTTACAGGCCCGAAATGCTGAATATAACCCTAAGgtatgtgagg ... ttgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttggtgttgttacctatttgctcaacgccttgttgggcactattgtgtacagCGTTTTGCAGCTGTTATTATGCGAATAAGGGAGCCAAAAACGACTGCCCTCATTTTTGCATCTGGTAAAATG
                 tattt  TA-rich tract