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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcaaactcattcgacttgctaataaggtttttgacgtatgtagtttttgtgatgtgctggagtttctgtctgtggaggaattttcttctgagtaatcgatatcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATTGTTAAAAG

Basic information

species Physcomitrella patens
transcript PP1S91_57V6.1
intron # 5
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|208378191|gb|DC918812.1|DC918812
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|208371949|gb|DC948352.1|DC948352
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|162184264|gb|FC359686.1|FC359686
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|37846274|gb|BJ604282.1|BJ604282
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|162180050|gb|FC356615.1|FC356615
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|162206599|gb|FC382357.1|FC382357
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|208381873|gb|DC923788.1|DC923788
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
EST: gi|37843587|gb|BJ601595.1|BJ601595
EST:     TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATG                         TACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT
genomic: TACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATT

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), 32 (downstream exon)
Score: 9

CTCTCCTGGTCCGGAATCGCTGGAGTGTGCTCTTTTTTCACTTGATGAGATACCATTCGATTCGATTGCATTCTCTTCTGTAACTGTCGCTCTAAAAATGgtgagtttca ... atcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATTGTTAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctggagtttctgtctgtggaggaattttcttctgagtaatcgatatcatttcagTACATTGAAGACGTCAAGGCAGGCCGAATCAGACATCACCATGGGGTTATTGTTAAAAG
                                              tcatttc  CT-rich tract
                       aattttctt  TA-rich tract