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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaacatgccttcattaagaacattcatccgaggtagtcaggctcgaagaagtgtgactatttctttgtttaatatcgccatttggagcatgttcacgctccgttgattacagctttgaatgtccacgtttctatcgtcatcatgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCACCTGTAGGGTTATCTTACAATTTTCAATCTTGAAAATGTTCACGCTTGCG

Basic information

species Physcomitrella patens
transcript PP1S65_2V6.3
intron # 6
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|67579208|gb|BJ951353.1|BJ951353
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|67696186|gb|BJ956419.1|BJ956419
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|67508564|gb|BJ941427.1|BJ941427
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|208359473|gb|DC954026.1|DC954026
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|37843824|gb|BJ601832.1|BJ601832
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGNCTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|67696077|gb|BJ956310.1|BJ956310
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|67691781|gb|BJ952014.1|BJ952014
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|67692649|gb|BJ952882.1|BJ952882
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|162232654|gb|FC409205.1|FC409205
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
EST: gi|37835112|gb|BJ593124.1|BJ593124
EST:     TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAG                         GAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC
genomic: TGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCAC

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: 33 (upstream exon), 34 (downstream exon)
Score: 7

TCGCACAACTAAGGTGAACTCGGGAATGGGTACAGGGACTATCACAAGCTTGATGGAGATGTTGGTATCAGGTGGTAGCCTGACTGGTGGTCTCACTCAGgtaagaaaca ... tgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCACCTGTAGGGTTATCTTACAATTTTCAATCTTGAAAATGTTCACGCTTGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccgttgattacagctttgaatgtccacgtttctatcgtcatcatgttgtgcagGAACCGCAATTGACGGCGAATGAGGCGTTTGACATTAACTCTCCTTTCCACCTGTAGGGTTATCTTACAATTTTCAATCTTGAAAATGTTCACGCTTGCG
   cgttgat  putative branch site (score: 7)
     ttgatta  TA-rich tract