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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattatactcaatgtgcgtggagcctgcgctttgggagtttttaagatgtaaaaaatagtataacagacgccatatactaattggttcatgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAATTGTTGTCAAGTTCTCTCACATTCGTCTGCGCAAATTTTAGTTCCAGCA

Basic information

species Physcomitrella patens
transcript PP1S78_210V6.2
intron # 1
splice site 3'
intron type U2

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|67571996|gb|BJ944820.1|BJ944820
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|162208443|gb|FC384198.1|FC384198
EST:     CCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100389276|gb|BY971026.1|BY971026
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100387007|gb|BY951406.1|BY951406
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|18368755|gb|BJ200840.1|BJ200840
EST:     ATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: ATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100396246|gb|BY972307.1|BY972307
EST:     GATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: GATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100406464|gb|BY955639.1|BY955639
EST:     GATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: GATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|208383574|gb|DC903531.1|DC903531
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100452904|gb|CJ975501.1|CJ975501
EST:     AATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: AATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|18354590|gb|BJ186647.1|BJ186647
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|162249724|gb|FC428164.1|FC428164
EST:     ATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: ATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100440758|gb|BY980578.1|BY980578
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGGGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100386465|gb|BY951261.1|BY951261
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100447463|gb|CJ971762.1|CJ971762
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100447741|gb|CJ972040.1|CJ972040
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|162199765|gb|FC375838.1|FC375838
EST:     GACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: GACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|100448830|gb|CJ973129.1|CJ973129
EST:     GAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: GAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
EST: gi|18331193|gb|BJ163202.1|BJ163202
EST:     CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAG                         GGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA
genomic: CGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAA

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), 35 (downstream exon)
Score: 12

CCTCTTTCGCATCCAGTGGTTGCGAATCCATTTATCTTCATCTCTTGTTGCGCCAGCAATTGATTCTGCCCTGTGACTGGGTTTTTGAGGAGTTGTTGAGgttggtcttg ... atgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAATTGTTGTCAAGTTCTCTCACATTCGTCTGCGCAAATTTTAGTTCCAGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatgtaaaaaatagtataacagacgccatatactaattggttcatgtttgcagGGTCTACAGCTGCTTACAGCAATTGGTGCCGTTTACTTCAAAGTAGCTTAATTGTTGTCAAGTTCTCTCACATTCGTCTGCGCAAATTTTAGTTCCAGCA
                                tactaat  putative branch site (score: 12)
      taaaaaatagtataac  TA-rich tract