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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtgtagatgtgaactttaggaaccattcttcggttctttgctaagtaatattgtggagagtggctggttgttgattttctctggttcttgtcatcagGTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGACCCATTTACAGAGAAGACACTTGCTTTTTCGTTAGTCAGTCAGGGGAAAC

Basic information

species Physcomitrella patens
transcript PP1S304_37V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S304_37V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 6
-------agagtgtagatgtgaactttaggaaccattcttcggttctttgc-taagtaatattgtgga--gagtggctggttgttgattt---tctctggttcttgt----------catcagGTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGACCCATTTACAGAGAAGACACTTGCTTTTTCGTTAGTCAGTCAGGGGAAAC
       |   | | |   |||    |       ||  ||  | | |   | | ||| | | | || |     |  ||| || ||||      |   |  | ||||           ||  ||||   || ||||| |||||  | || ||||| || |||||| | ||||| ||||| ||||| |||||||||   ||||||||||| ||||||||||| ||
gtatgccaacttattgtcctgactccttatgtagatattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcatccttgcattatttggacaatagGTATTCCTGTGACTATGGAGGTTGCAAGTGACTTGCTGGACAGACAAGGTCCCATCTACAGGGAAGACACTGCATTTTTCGTTAGCCAGTCAGGGGAGAC
















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|162164178|gb|FC339601.1|FC339601
EST:     GAGTTATCACGCCGGATTGGCAACACGAGCCCTTGTGGAAGAGCTGTCAG                         GTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGAC
genomic: GAGTTATCACGCCGGATTGGCAACACGAGCCCTTGTGGAAGAGCTGTCAGgtactactag ... ttgtcatcagGTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGAC
EST: gi|162163432|gb|FC339966.1|FC339966
EST:     GAGTTATCACGCCGGATTGGCAACACGAGCCCTTGTGGAAGAGCTGTCAG                         GTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGAC
genomic: GAGTTATCACGCCGGATTGGCAACACGAGCCCTTGTGGAAGAGCTGTCAGgtactactag ... ttgtcatcagGTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGAC

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: 24 (upstream exon), 28 (downstream exon)
Score: 4

TTACGAACTATCCGACGTAGTAGGAGGATCCTCTTCATTGGGTGTGGTACGAGTTATCACGCCGGATTGGCAACACGAGCCCTTGTGGAAGAGCTGTCAGgtactactag ... ttgtcatcagGTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGACCCATTTACAGAGAAGACACTTGCTTTTTCGTTAGTCAGTCAGGGGAAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtaatattgtggagagtggctggttgttgattttctctggttcttgtcatcagGTGGACCGGTGACGATGGAATTGGCTAGTGATTTACTGGACCGTCAAGGACCCATTTACAGAGAAGACACTTGCTTTTTCGTTAGTCAGTCAGGGGAAAC
                          tgttgat  putative branch site (score: 4)
                                ttttctctggttctt  CT-rich tract
                            ttgatttt  TA-rich tract