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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaagacattgtaatagtggcctaacctttgaaccttcgttttggttgacgaggttttctatgtgtgccttgattcatgtttttctttaatcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAACTACAAAACTATATTCGCATTTCTGTTGGGAAGCCAGAACAGACTGACG

Basic information

species Physcomitrella patens
transcript PP1S175_129V6.1
intron # 9
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|162213237|gb|FC389317.1|FC389317
EST:     ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAG                         GCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
genomic: ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
EST: gi|162215955|gb|FC392372.1|FC392372
EST:     ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAG                         GCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
genomic: ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
EST: gi|37836183|gb|BJ594191.1|BJ594191
EST:     ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAG                         GCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
genomic: ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
EST: gi|162213238|gb|FC389318.1|FC389318
EST:     ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAG                         GCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
genomic: ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
EST: gi|162215954|gb|FC392371.1|FC392371
EST:     ACTTCATTTTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAG                         GCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
genomic: ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
EST: gi|208395168|gb|DC915977.1|DC915977
EST:     ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAG                         GCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA
genomic: ACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAA

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), 30 (downstream exon)
Score: 12

TGTGAAGCTGAAAGAGTTTTCCTTTCTGGAGCCATATCCCAGTCATGCCAACTTCATTCTGTGTTCCGTAACGGGCAACAAAACTGCCAGGGAACTGAAGgtaaaacctt ... tcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAACTACAAAACTATATTCGCATTTCTGTTGGGAAGCCAGAACAGACTGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacgaggttttctatgtgtgccttgattcatgtttttctttaatcatgtacagGCTGCACTTGCTAAGGACGGAGTAATGGTTCGCCACTACGAGAAGGCCGAACTACAAAACTATATTCGCATTTCTGTTGGGAAGCCAGAACAGACTGACG
                                       ctttaat  putative branch site (score: 12)
                               atgtttttctttaat  TA-rich tract