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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctaaaatccatcctctctgccgtcctgcgactttcaattttgtctttcattcctcctgaacgggggaaattcgagaggttgagagagttcatggttttttggtcgtcgtgcgaggaatggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGAGATGGCATCCGGCACATCACCTGCACGGATTTGTCGACAGTGGCCGTGG

Basic information

species Physcomitrella patens
transcript PP1S41_202V6.1
intron # 2
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|67508128|gb|BJ940999.1|BJ940999
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
EST: gi|100438774|gb|BY961796.1|BY961796
EST:     CAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
genomic: CAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
EST: gi|162180625|gb|FC356982.1|FC356982
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
EST: gi|67577757|gb|BJ949924.1|BJ949924
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
EST: gi|100436243|gb|BY979451.1|BY979451
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
EST: gi|18365754|gb|BJ197831.1|BJ197831
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAG
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCT-GGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAG
EST: gi|208352453|gb|DC910181.1|DC910181
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA
EST: gi|208353897|gb|DC914065.1|DC914065
EST:     ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGG                         GTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGANCGAGGACATGTACAGA
genomic: ACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGA

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: 35 (upstream exon), 18 (downstream exon)
Score: 2

GGACGAACGCTTCCAAGGTGAACAGCACTACGAATGGTTCAAGAACTACTCGCATTTTCGACATCTTGTGTTGAAGCACATCAAACCGACCGACAGGgtatgcctaa ... atggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGAGATGGCATCCGGCACATCACCTGCACGGATTTGTCGACAGTGGCCGTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagaggttgagagagttcatggttttttggtcgtcgtgcgaggaatggccacagGTGCTGGAGGTCGGTGCAGGCTCGTCGAGGCTGAGCGAGGACATGTACAGAGATGGCATCCGGCACATCACCTGCACGGATTTGTCGACAGTGGCCGTGG
                       tttttt  TA-rich tract