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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacattacattttttacatcattttcgagattcggttagtagtgtaggcttgtacgtagtgctttggcaaccaatggtaacctccgtctacactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTTGATTGTCACAACCATGAATGGTAATGTTTATTGTTTCCAGACACCTGCT

Basic information

species Physcomitrella patens
transcript PP1S334_25V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S334_25V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA03G14690.1 (Glycine max), 3'ss of exon 12
ttacattacattttttacatcattttcgagattcggttagtagtgtaggcttgtacgtagtgctttggcaaccaatggtaacctccgtctacactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTTGATTGTCACAACCATGAATGGTAATGTTTATTGTTTCCAGACACCTGCT
               ||    ||| |  |  |    |   | |  || |||| |  ||  | ||||    |      || |  | |   |    |  |||||||||||||||  | ||||||||||| ||||| || |||||  | ||| | ||||||||||| |||||||| ||||| |  || |||   || ||  ||
--------------gtaagagattctttaactgttatctctcggatatgctt-tctgttctactttcttga-----agttatgtgccattttttttacagGTATAGCATGGTCTTGGCAGACAATGTTGATGGTGGGGATGATCTTGATCTAATTGTCACAACAATGAATGGCAATGTCTTCTGCTTCTCAACCCCATCT

upper sequence: PP1S334_25V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 3'ss of exon 10
ttacattacattttttacatcattttcgagattcggttagtagtgtaggcttgtacgtagtgctttggcaaccaatggtaacctccgtctacactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTTGATTGTCACAACCATGAATGGTAATGTTTATTGTTTCCAGACACCTGCT
     | |  | |  | ||  | | |  |  ||  |||  || |||    || | |  | |   ||   ||   ||     |||   |         ||| ||||||||||| || || |||||||| ||||| || |||||  | ||| | ||||| |||||||||||||| ||||| | ||| ||    || ||||||
----gtaagttatcctccactactattcatgtttagttt-tactgtttaatttttcaaaatttgtttaaaat--ataaatgcctttatt-------acagATATAGCATGGTCCTGGCGGACAATGTTGATGGTGGAGATGATCTTGATCTTATTGTTACAACCATGAATGGCAATGTATTTTGCTTTTCAACTCCTGCT
















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|162184192|gb|FC359653.1|FC359653
EST:     ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTC                         GTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
genomic: ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTCgtaagttttc ... acactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
EST: gi|162216337|gb|FC392130.1|FC392130
EST:     ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTC                         GTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
genomic: ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTCgtaagttttc ... acactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
EST: gi|208365360|gb|DC954801.1|DC954801
EST:     ANTGAAGGTAGTTCTGGCTGTGCTGNAGCTATCGACA-TGGGGAAACCTC                         GTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
genomic: ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTCgtaagttttc ... acactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
EST: gi|162174410|gb|FC350481.1|FC350481
EST:     ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTC                         GTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT
genomic: ATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTCgtaagttttc ... acactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTT

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: 22 (upstream exon), 26 (downstream exon)
Score: 2

GAAAAGGGCTGACCATCGCTGTCACATCATTTGATGGCTACTTTTACCTGATTGAAGGTAGTTCTGGCTGTGCTGAAGCTATCGACATTGGGGAAACCTCgtaagttttc ... acactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTTGATTGTCACAACCATGAATGGTAATGTTTATTGTTTCCAGACACCTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggcttgtacgtagtgctttggcaaccaatggtaacctccgtctacactcgcagGTATAGCATGGTGCTAGCAGACAATGTGGATGGAGGCGATGACTTGGATTTGATTGTCACAACCATGAATGGTAATGTTTATTGTTTCCAGACACCTGCT
                              tggtaac  putative branch site (score: 2)