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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatgaggttaatttggtacagcttggggaacagcctatattttgtaatccgctaactctttctcggctcgtaacacggatggcgtttactctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG

Basic information

species Physcomitrella patens
transcript PP1S397_39V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S397_39V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 2
-tccatgaggttaatttggtacagcttggggaacagcctatattttgtaatccgctaactctttctcgg-ctcgtaacacg-gatg-gcgtttactctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG
  ||   |    |||||   ||  | ||   |    | |  ||  | |||   | |  |  ||  | |  || | ||   | |||| |   |||    || ||||||||||||| ||||| || ||||| |||||||||||||| ||    ||||| ||||| |||   ||||| |  || |||  ||  || || |||
gaccgcaatagcaatttaaaac--catgcataggtacatgaataat-taagttgttttcaattcattgaacttggaaattgtgatgtgaaattaaaacga-cagTGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAG
















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|37835032|gb|BJ593044.1|BJ593044
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
EST: gi|162267551|gb|FC444302.1|FC444302
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
EST: gi|18365047|gb|BJ197121.1|BJ197121
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATG
EST: gi|18336855|gb|BJ168878.1|BJ168878
EST:     GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTT                         TGCAGCACACTAAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGAT
genomic: GATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACT-AGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGAT

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), 34 (downstream exon)
Score: 31

ATTTTGAAGGAGATCGAGTCTGACTTGGCTCGTTTCAAATGCGGCATTGCTCATCTCTTTTgtgagtaaca ... ctctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatccgctaactctttctcggctcgtaacacggatggcgtttactctgatcagTGCAGCACACTAGTGCGTCGCTTACAATCAATGAGAATTACGATGGCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG
                        tcgtaac  putative branch site (score: 31)
                                         tttactct  putative PPT