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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcgtcacttattgaatcgtaaggaaggccgtcattcgtatttacgatgaccttttggagggattgaaggagagttactgatatggttgtgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCCAGGGCGCAGGACTTTTTGTTCATTTCTGGTACCAAG

Basic information

species Physcomitrella patens
transcript PP1S331_37V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S331_37V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G14680.1 (Arabidopsis thaliana), 3'ss of exon 3
aatcgt-cacttattgaatcgtaaggaaggccgtcattcgtat-ttacgatgaccttttggagggattgaaggagagttactgatatggttgtgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCCAGGGCGCAGGACTTTTTGTTCATTTCTGGTACCAAG
    ||  | | || ||| |   |  |    |    || |||| || |    |   ||| |     ||||       || ||| | |   |   | ||||||||||| || ||||| || ||  |  |  ||||||| ||||| ||||| || ||||| |||||||| |||||||||||||| || |||
----gtatattcatagaaaccgcataatactcaaacttggtatcttccttcaaagatttaggctttttgagttctgatttctggtttcaat---tggtgtagGTTGCTGCGTACGATAAGACACAAGGAAAGATGGCTTTCTTTGATCCCTCAAGGGCTCAGGACTTCTTGTTCATTTCTGGCACTAAG
















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|162162006|gb|FC338589.1|FC338589
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37849069|gb|BJ607077.1|BJ607077
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|162176154|gb|FC351090.1|FC351090
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37853261|gb|BJ611269.1|BJ611269
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37848002|gb|BJ606010.1|BJ606010
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37850021|gb|BJ608029.1|BJ608029
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|67691750|gb|BJ951983.1|BJ951983
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|208372292|gb|DC948481.1|DC948481
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37821007|gb|BJ579073.1|BJ579073
EST:     TGCTCAGCATGGCTCNTGNCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37850056|gb|BJ608064.1|BJ608064
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|162176153|gb|FC351089.1|FC351089
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
EST: gi|37822990|gb|BJ581056.1|BJ581056
EST:     TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGG                         GTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC
genomic: TGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCC

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: 31 (upstream exon), 35 (downstream exon)
Score: 30

CCACCCCACTGCCGGGCGCGATCTCTACGACGCAGACCACGGAAAGATGGTGCTCAGCATGGCTCCTGGCCTTGAGAAGCTCAACATTCTGCCCTTCAGGgtaattccag ... tgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCCAGGGCGCAGGACTTTTTGTTCATTTCTGGTACCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatgaccttttggagggattgaaggagagttactgatatggttgtgttgtgtagGTTGCGGCTTACGACAAAACGAAGAGTCAGATGGCATTCTTCGATCCATCCAGGGCGCAGGACTTTTTGTTCATTTCTGGTACCAAG
                               tactgat  putative branch site (score: 30)