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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcacccactattttcaatccctatgttcatagttgtgacacgttccaagttgttggatactcgtggaagccttttgtaactgttctttttaattttgaattcatgagtggacagttttggtttttggtcgagtctcaaggctttgtttctgtcttacgagttgtatatgtggcgcctggatgtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAAATCTGGTCAAGAATAGGCGCGAAAGTCAATCCTTTGATTCATCGCTTTG

Basic information

species Physcomitrella patens
transcript PP1S42_16V6.1
intron # 8
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|162237826|gb|FC412479.1|FC412479
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTTTACTATAGAGCCCCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|162231291|gb|FC406532.1|FC406532
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|162237827|gb|FC412480.1|FC412480
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|37847707|gb|BJ605715.1|BJ605715
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|18336481|gb|BJ168503.1|BJ168503
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|162154890|gb|FC331932.1|FC331932
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|37836287|gb|BJ594295.1|BJ594295
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|208371600|gb|DC952242.1|DC952242
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|208399430|gb|DC924860.1|DC924860
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|37835310|gb|BJ593322.1|BJ593322
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
EST: gi|162154889|gb|FC331931.1|FC331931
EST:     GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAG                         TTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA
genomic: GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAA

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), 29 (downstream exon)
Score: 8

GCCTCAACGTAATATTGTTCAAGCGTTGATCTACTGGCAGgttggcaccc ... gtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAAATCTGGTCAAGAATAGGCGCGAAAGTCAATCCTTTGATTCATCGCTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggctttgtttctgtcttacgagttgtatatgtggcgcctggatgtcttttcagTTATTGAAGCTCTACTATAGAGCACCAAACACTTCTTTGTATCATCATCAAATCTGGTCAAGAATAGGCGCGAAAGTCAATCCTTTGATTCATCGCTTTG
              gtcttac  putative branch site (score: 8)
 tgtcttttc  putative PPT
 ttgtatat  TA-rich tract