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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgcagtttcattctgcattgaattccagaggttgacgagtttgcgctgcagttatggcttcgacaactccgtccaagaataagtatattccacgtgcacgtctgctaattggggaccaaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCTGCACCGGACAAAGGCGACGATTATCGGATTGTTTGACATTGGTAATGTG

Basic information

species Physcomitrella patens
transcript PP1S36_62V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S36_62V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagtcgcagtttcattctgcattgaattccagaggttgacgagtttgcgctgcagttatggcttcgacaactccgtccaagaataagtatat-tccacgtgcacgtctgctaattggggaccaaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCTGCACCGGACAAAGGCGACGATTATCGGATTGTTTGACATTGGTAATGTG
            |  ||||||       |  |  | ||       | |  | | |  | || |  | |   |       |   | | ||| ||  |||   |  |  |||| |  |    |  ||||    |||||  | ||  || || | |  ||||| || |||||||| |||||||||||||||||||||||||| ||  | || ||  |||||||    || |  |  
-----------gtatattctgttccttgtatctcaagtcatta--tctctgtttctttcatagggttgcttatatgtcacgtaactgagtttaaatccttttctatttctgatttt----gttcaaa----agGTCAATTCATCTGCTGTTCTATTGGATTCTATTCGAGAATGTGATGTCGCTGCACCGGACAAAGGCCACTCTCATTGGTCTGTTTGAGGCAGGAAGGGCT
















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|37848471|gb|BJ606479.1|BJ606479
EST:     GTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCCACCCCCCAA                         GTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGC
genomic: GTATGTGCCGTCGATCATCACACTGCTGAACGCCATCA-CCA-CCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGC
EST: gi|37847359|gb|BJ605367.1|BJ605367
EST:     GTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCCACCCCCCAA                         GTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGC
genomic: GTATGTGCCGTCGATCATCACACTGCTGAACGCCATCA-CCA-CCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGC
EST: gi|208382282|gb|DC919270.1|DC919270
EST:     GTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAA                         GTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCT
genomic: GTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCT
EST: gi|208354350|gb|DC926569.1|DC926569
EST:     GTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAA                         GTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCT
genomic: GTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCT
EST: gi|37839708|gb|BJ597716.1|BJ597716
EST:     GTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCCACCCCCCAA                         GTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGC
genomic: GTATGTGCCGTCGATCATCACACTGCTGAACGCCATCA-CCA-CCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGC
EST: gi|67727759|gb|BJ978018.1|BJ978018
EST:     GTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAA                         GTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCT
genomic: GTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCT

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: 34 (upstream exon), 33 (downstream exon)
Score: 15

TTCCTGCTTCCGTGTTGGTCCCCGAGGTCGACCTACCATTCTGGGGAGCTGTGTATGTGCCGTCGATCATCACACTGCTGAACGCCATCACCACCCCCAAgtaagtcgca ... caaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCTGCACCGGACAAAGGCGACGATTATCGGATTGTTTGACATTGGTAATGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaagaataagtatattccacgtgcacgtctgctaattggggaccaaattgcagGTCTCTACACTTGTTGGTGTTCTGGATCCTGTTCGAGAACGTGATGTCGCTGCACCGGACAAAGGCGACGATTATCGGATTGTTTGACATTGGTAATGTG
                               tgctaat  putative branch site (score: 15)
      aataagtatatt  TA-rich tract