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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatattagttggttttgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG

Basic information

species Physcomitrella patens
transcript PP1S197_115V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 8
---agaatattagttggttttgttttggtttgactgtg-tagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggtta-tgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
   | || |   |||        |||  | | | || | |  |  ||   |    || ||  |  | |   ||     |||  || ||  ||||  ||  |||||| ||||||||||| ||||||||||| || ||| ||||||| ||||| |||||||| || ||  | || ||| | || |||||||||
gtaataacacatgttctcaccaatttactataattgagctgaacctgtcgtctgggtttcttatcttaaaatg-----gttcgatgctaatgttctttcctgcagTTAAAACAAACGATATGATGTTGGTCATATACTTGTCTTCTCTTATCCGGAGTGTCATCGCACTCCATAACTTGATCAATAACAAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G061745_T02 (Zea mays), 3'ss of exon 7
agaatattagttggttttgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggtta-tgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
  ||| ||   |   ||| || || ||| ||     |||  |  | |||   ||  |    | |   |||    |    ||  ||   ||  ||  ||||||||||||||||||||||||||||||||| ||||||||||| || || ||||| || |||||  | |||||  | || || || |||
gtaatcttgcat--ctttcttctgatttaacataacagaccttatcttc---tcagaatccttattttgcagcagccttatgtttcctttctttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 8
agaatattagttggttttgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggtta-tgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG--------------
  ||| ||   |   ||| || || ||| ||     |||  |  | |||   ||  |    | |   |||    |    ||  ||   ||  ||  ||||||||||||||||||||||||||||||||| ||||||||||| || || ||||| || |||||  | |||||  | || || || |||              
gtaatcttgcat--ctttcttctgatttaacataacagaccttatcttc---tcagaatccttattttgcagcagccttatgtttcctttctttggtgcagTGAAAACAAACGACATGATGTTGGTGATATACCTGTCTTCTCTGATCCGGAGCGTCATTGCGCTTCACAATTTAATCAACAATAAGGTTGATTCATATCT

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 5
agaatattagttggttttgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
  ||| ||   |  |||| || || ||| ||    | ||  || | ||    | |      || ||   || |||||       | | |   || | |||||||||||||||||||||||||||| || || |||||||| || || |||||||| |||||  | |||||  | || || || |||
gtaatcttgcatcttttt-ttctgatttaacataattgacctgatcttttcatattc----tcgggagccttatgttg------tctttcttttgtacagTGAAAACAAACGACATGATGTTGGTAATATATCTGTCTTCTCTGATCCGGAGTGTCATTGCGCTTCACAATTTGATCAACAATAAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 8
agaatattagttggttt-tgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
         ||  |||| || | |  |||   | | || ||| || |    | ||| |||  |        | || || | |   | | |    | ||||||||||||||| ||||||||| | || || || || || ||||| ||||||||||| |||||  | |||||| | || || ||||||
---------gtgagtttctgctatcattttgatat-tatattgggctgc--tttcttagatct-gcttcattaatctttactgtatttataa--tgtgcagTGAAAACAAATGACATGATGCTCGTTATCTATCTATCATCCCTCATTCGGAGTGTAATTGCGCTCCACAACTTGATCAACAACAAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 8
agaatattagttggttttgttttggtttgactgtgtagatttggttttcatgtctcagaagtcagggtgctcat-gttaaatacttgtg-ttggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
      | ||       | || |  | || || ||    | |  |  |||||||    || |       ||| | | |  ||   ||   ||   ||||||||||||||||| || ||||||||||| ||||| || || || || || || |||||||| ||| | |||||| | || |||||||||
-----gtgaggccaagatattattttctgcctttg---gtatcttcatcatgtcatctaacttttcccactctttgatccatgtgtgcccttttctatgcagTGAAAACAAATGATATGATGTTGGTTATTTATCTTTCATCTCTCATCCGAAGTGTTATAGCTCTCCACAACTTGATCAATAACAAG

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|208351962|gb|DC925771.1|DC925771
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
EST: gi|7693546|gb|AW761652.1|AW761652
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
EST: gi|208368978|gb|DC955063.1|DC955063
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
EST: gi|162212342|gb|FC388070.1|FC388070
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
EST: gi|7648296|gb|AW739279.1|AW739279
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
EST: gi|208371459|gb|DC955795.1|DC955795
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
EST: gi|37826136|gb|BJ584148.1|BJ584148
EST:     CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTG                         TGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA
genomic: CAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGA

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: 35 (upstream exon), 35 (downstream exon)
Score: 6

GATGTATTCAACCTGCTACCCAACCTCAATGTCCATGAGCTTGTTAAATCCTTTGCTGgtgagttaat ... ggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgtctcagaagtcagggtgctcatgttaaatacttgtgttggttatgcagTGAAAACAAACGACATGATGTTGGTGATTTACCTGTCTTCCCTTATTCGGAGTGTTATTGCTTTACACAACCTCATAAATAACAAG
                           atgttaaata  TA-rich tract