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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgcatctaatccctcttatgctgccaaacagcaaactgatgtggcctggtgttaacatttccaattatgcctgagtcaaaatatatagcttctactaataccatcatattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGAACGATCCCACAACAAAGATAGGGGTGGCTGTATTCCAGAAACCTACAGA

Basic information

species Physcomitrella patens
transcript PP1S99_226V6.2
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|162179970|gb|FC356041.1|FC356041
EST:     GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAG                         ACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
genomic: GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
EST: gi|100443123|gb|BY981749.1|BY981749
EST:     GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAG                         ACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
genomic: GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
EST: gi|162176974|gb|FC353651.1|FC353651
EST:     GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAG                         ACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
genomic: GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
EST: gi|162166161|gb|FC342598.1|FC342598
EST:     GTTC-AATATGGAAAG                         ACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
genomic: GTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
EST: gi|162159293|gb|FC334613.1|FC334613
EST:     GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAG                         ACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
genomic: GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
EST: gi|100443095|gb|BY981721.1|BY981721
EST:     GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAG                         ACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA
genomic: GGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGA

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), 35 (downstream exon)
Score: 10

CTTGTTGAGCTGAATCGCGTTCTAAGACCAGGGGGCTACTTTCTGTGGTCGGCAACCCCTGTGTACTGGAAGGACGAGGAGAACGTTCAAATATGGAAAGgttcgcatct ... catattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGAACGATCCCACAACAAAGATAGGGGTGGCTGTATTCCAGAAACCTACAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaattatgcctgagtcaaaatatatagcttctactaataccatcatattgcagACACAAAAGTTATCACAGAAAGACTGTCTTGGAAGTTGGTGGCCAAGAAGAACGATCCCACAACAAAGATAGGGGTGGCTGTATTCCAGAAACCTACAGA
                                 tactaat  putative branch site (score: 10)
              agtcaaaatatata  TA-rich tract