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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S123_138V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 10
gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
                     ||    | |        || || ||  |     |       |  |||||  ||||   ||     |||  |   | | |      |||    |  | |||||||| ||||||||||| || ||||| |||||||| |||||| | || || ||| |||| |||||||||||||| || ||||| ||||| |||||||||
---------------------actgctatggcacccctccaatatctgacaagctggaacaaaaaatctgttttgtcatttcactgtatggttttcttttacaaaagttatgttgtttcagGATGCAAAAAAAGGAGTTCTTTTTATCGACTTCCCTCCTGTTTTGCAACTTCAGCTAAAACGTTTTGAGTATGATTTCATGCGTGACACGATGGTGAAG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 4
-------------------------------------gtactgaattttcatataagtacaatcaggtg----------gatgaccctatttcacaggcctt-taggt--tcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgt----cctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
                                        || |  ||   |||  |    ||    ||          ||| | | | || ||      || | |||  |   | |   | | || | ||||||| ||| |   | ||    | | ||    |    | | |||||||| |  || ||  |  | || || || ||||| |||||||||||||| |||||||| || |||||||| || | || ||||||||| ||||| |||
gtaaaacctgaacatgtgtttttgcttttttgttgtcaggctaaccttcagtatgtgcgttattttttgttaattgtttgattatctttttacatcacttttgttggttgttgttgttaaattcgtattttagaatgattattttcctagaacgtgattatgattaccctttcagGATGCTAGGAAGGGTATGTTGTTCATTGATTTCCCACCTGTTCTTCAGCTTCAGTTAAAACGGTTTGAGTACGATTGTACGCGAGACACTATGGTAAAG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 8
gtactgaattttcatataagtacaatcaggtgg-atgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
      |  |||||   ||| |  | ||| ||  |       |||| ||     | ||   | | |  ||||  | | ||||| |     |   || |  | ||     || |    | |||||||| |||||||| || ||||| |||||||| || || |||||||| || ||| | ||| | ||||| || || |||||| | |||||||||||||||
------atatttca---aagcaggaacagctgataaagttgcatttgactaatttatattgttact--ctgaact-tatcttata-----ttggaatacttttt-----ttattattttcagGATGCAAAAAAAGGTGTTCTATTCATAGACTTTCCACCAGTTCTTCAACTTCAGCTCAAGAGGTTTGAATACGATTTTATGAGGGACACAATGGTGAAG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 8
gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
           | |   ||||  ||| |     |    ||||  |   |    |  |  | ||||  |    |   ||||||       |||      | ||||   | | | |  | |||||||| |||||||| || || || || ||||| || || |||||||| || ||| | ||| | ||||| |||||||||||| | ||||| |||||||||
----------ctaagccaagt-taattaacc--accgacctaactgttattattacaaatgcagtccccttatctagtcttaa------tctgggggaa-cttgatttctat-tgtttcagGATGCAAAAAAAGGTGTTCTTTTCATTGACTTTCCACCGGTTCTTCAACTCCAGCTCAAGAGGTTTGAATATGACTTTATGAGGGACACCATGGTGAAG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 8
gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
      | ||||| |      |  |||   |  |||  | |  |    | |  ||| | ||   | |    |  |      |   ||  || |  ||||| || |  ||    | || |||||||| || || || ||| ||||||| |||||||| || |||||||| || ||| ||||||| |||||||||||||| ||||| ||||| |||||||||
------acttttctt-----catgatcgaatctatgttcttgct----aagttttttgatttttttttcctgaag------atggtttctcaagccatatttttgaattgtgttacttcagGATGCTAAGAAGGGTGTCTTATTTATTGACTTCCCACCAGTTCTTCAACTTCAGCTAAAGCGGTTTGAGTATGACTTCATGCGGGACACTATGGTGAAG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ18164 (Selaginella moellendorffii), 3'ss of exon 6
gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
                                                                        |||| | |     |   | | || |    ||   | |||| || |  |||||||    || || || || ||| | || || ||||||||||| ||||| ||  | ||||| ||||| ||||| ||| |||||||||||||||| |||
----------------------------------------------------------------------gtttgtttttcgtgttccatgtcaagaaggtttaatggttgtttcttttagGATGCACGCAAGGGCGTGCTCTTTGTGGATTTTCCCCCTGTTCTCCAGCTTCAACTCAAGCGGTTTGAATATGATTTTGTGCGAGACACAATGGTTAAG

upper sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 6
gtactgaattttcatataagtacaatcaggtggatgaccctatttcacaggcctttaggttcagtatctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
                                                                        |||| | |     |   | | || |    ||   | ||||  | |  |||||||    || || || || ||| | || || ||||||||||| ||||| ||  | ||||| ||||| ||||| ||| |||||||||||||||| |||
----------------------------------------------------------------------gtttgtttttcgtgttccatgtcaagaaggtttaatggttgttgcttttagGATGCACGCAAGGGCGTGCTCTTTGTGGATTTTCCCCCTGTTCTCCAGCTTCAACTCAAGCGGTTTGAATATGATTTTGTGCGAGACACAATGGTTAAG

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|67575556|gb|BJ948380.1|BJ948380
EST:     AACGGTTGGAGGGCGAGAACAAATACCACGCCGAACAATTTGGGTTGCAG                         GATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTA
genomic: AACGGTTGGAGGGCGAGAACAAATACCACGCCGAACAATTTGGGTTGCAGgtactgaatt ... tgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTA




















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: 22 (upstream exon), 14 (downstream exon)
Score: 1

GAAAGGATGCAAGGATGTATATGAATCTTTTGACAAGTATGTTGAAGTAGAACGGTTGGAGGGCGAGAACAAATACCACGCCGAACAATTTGGGTTGCAGgtactgaatt ... tgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgagttgtgtcttagaattattctaaacatatcttggggtttgtgtcctgcagGATGCGAAAAAAGGAGTCCTATTTATAGACTTCCCCCCTGTTCTTCAGCTACAGTTAAAGCGTTTTGAGTATGACTTTATGCGAGACACAATGGTGAAG
                      ttctaaa  putative branch site (score: 1)
             ttagaattattctaaa  TA-rich tract