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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaagtcacgtaggataggccttcgtgttcctcactgtcagcagtccatgctgtcgcaagagtatggatctcacgtgctcctggcacgttgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG

Basic information

species Physcomitrella patens
transcript PP1S387_39V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S387_39V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 7
gttaagtcacgtaggataggccttcgtgttcctcactgtcagcagt--ccatgctgtcgcaagag-tatgg-atctcacgtgctcctggcacgt-tgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG
       || | |  || | | |  |   ||    ||||    | |   |||    | ||| ||  |||    | || |    |  |  |  |  |  | |||||||  | |  ||||| | ||     || |||||||||||||||||||||||||||||||||
-----tccatgcataattgccatatgatatcacatctgttttaaataatcataagattgcatgatctatcctgtttccccaaatattaacttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG

upper sequence: PP1S387_39V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 6
gttaagtcacgtaggataggccttcgtgttcctcactgtcagcagt--ccatgctgtcgcaagag-tatgg-atctcacgtgctcctggcacgt-tgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG
      ||  | |  |  | | || |   |     |||  |  | |   | |   || ||| ||  |||    | || |    |  |     |  |  | |||||||  | |  ||||| | ||     || |||||||||||||| ||||||||||||||||||
-----ttcctgcataactgccatttgatattgcatctggtataaataatcgtaaggttgcatgatctatcctgtttccccaaatattaatttgcatattttgcagATAACAGGGCAATCATGTCCATTATCATTCAAGGGAAGCCCCTATTGGATGGCTCCTGAG

upper sequence: PP1S387_39V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 8
gttaagtcacgtaggataggccttcgtgttcctcac--tgtcagcagtccatgctgtcgcaagagtatggatctcacgtgctcctggcacgttgc----tctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG
      ||  ||   || |   |||   |||   |   | | |  | ||||    || |||  | | ||        |  || ||   ||  | |    | |||||||  | |  ||||| | |||   ||| |||||||||| |||||| |||||||||||||||
---gcatctggttt-attgattttctaattctaaatgatttaattaatccaaag-gttgcataatt-tgtcctgtttgccctacttataccctacataatttgcagATAACAGGGCAATCGTGTCTATTGTCATTCAAGGGAACCCCTTACTGGATGGCTCCTGAG

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|162180333|gb|FC355338.1|FC355338
EST:     TAGACACCAACGGGATGGTGAAACTTGCCGACTTCGGCATGGCTAAGCAT                         ATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATG
genomic: TAGACACCAACGGGATGGTGAAACTTGCCGACTTCGGCATGGCTAAGCATgtatgtctgc ... tgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATG




















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: 12 (upstream exon), 34 (downstream exon)
Score: 2

GGATATCAAGGGCGCCAACATTCTTGTAGACACCAACGGGATGGTGAAACTTGCCGACTTCGGCATGGCTAAGCATgtatgtctgc ... tgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgctgtcgcaagagtatggatctcacgtgctcctggcacgttgctctgcagATTTCTGCTCAATCTTTTCTCCAGTCTTTCAAGGGAAGCCCTTATTGGATGGCTCCTGAG
                       atctcac  putative branch site (score: 2)
                                            ttgctct  putative PPT