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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttcatatggttgttatttttctcttgtcttaaaattttaagatggttttatttttgtagttcgtctgtgatgtagtagaaaattcctctggcttcttcggtggttgatatcctcacttcttgttgcatactgtcactcataagcttttttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG

Basic information

species Physcomitrella patens
transcript PP1S107_71V6.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S107_71V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
gtaatttttcatatggttgttatttttctcttgtcttaaaattttaagatggttttatttttgtagttcgtctgtgatgtagtagaaaattcctctggcttcttcggtggttgatatcctcacttcttgttgcatactgtcactcataagcttttttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG
                                                               |  |  || |||||| ||  | | ||||| | |   |  |    |  |  |||   | |  | |  |  ||||     | ||| |   || |  |    |||||||||||  | |||||| | ||||| |||||||||||||||||||||||| |||| || ||  ||||||| || ||| |||| || || ||| |  || 
--------------------------------------------------------------ctgat--gtatgtgatatataatataattcgtttt-ttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatgcagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT

upper sequence: PP1S107_71V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 18
gtaatttttcatatggttgttatttttctcttgtcttaaaattttaagatggttttatttttgtagttcgtctgtgatgtagtagaaaattcctctggcttcttcggtggttgatatcctcacttcttgttgcatactgtcactcataagcttttttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG
                                                                      |     |  || ||    |||  | |   || |    |  |  |||   | |  | || |  ||||     | |   |   || | ||    |||||||||||  | |||||| |  |||| |||||||||||||||||||||||| |||| || ||  ||||||| || ||| |||| || || ||| |  |  
-------------------------------------------------------------------gtattcaccagata-tatgtgattttttt---ttataaaattatgtatagaataatatattttctcataaatggatttcaacttttgtgtggatgcagGTTGGTGGCATCTATGTTAGGCTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCGT

upper sequence: PP1S107_71V6.1 (Physcomitrella patens), 3'ss of exon 20
lower sequence: EFJ24089 (Selaginella moellendorffii), 3'ss of exon 18
gtaatttttcatatggttgttatttttctcttgtcttaaaattttaagatggttttatttttgtagttcgtctgtgatgtagtagaaaattcctctggcttcttcggtggttgatatcctcacttcttgttgcatactgtcactcataagcttttttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG
                                                                                               | | || ||      || || |||||| |  ||| |  ||  |  | ||  ||    ||  ||    |||||||| |||||||| ||  | ||||||||||||||||| || || |||||||| ||||| ||| |||| || || ||  | || || || |||||  | |
----------------------------------------------------------------------------------------------gtagattttt------ttaat-tcctcaatctttgatctatcgtaacgcttttatttcttgctg--tgcagGTTGGCGGAGTGTACGTAAGATTGTTCCTGAAAGATCCAAAGTTTCCTCTTCGGAATCCCAAGAGGTTTTTGGAAGGACTTCTGGATCAGTATGTAGCCG

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|162246193|gb|FC423603.1|FC423603
EST:     ATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAG                         GTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTT
genomic: ATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAGgtaatttttc ... ttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTT
EST: gi|162198571|gb|FC374756.1|FC374756
EST:     ATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAG                         GTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTT
genomic: ATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAGgtaatttttc ... ttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTT
EST: gi|162150554|gb|FC326410.1|FC326410
EST:     ATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAG                         GTTGGTGGAGTGTATGTTCGCTTGTTCCTGANAGATCCCAAATTCCCTCTT
genomic: ATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAGgtaatttttc ... ttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTT

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: 30 (upstream exon), 33 (downstream exon)
Score: 4

GGCAGCCGATCTGTATAAAGAGCAAACCAAGGGTAAAGTGATCGAATGGGATCTTCCTGAGAGTTCATCTGGGGAGCAAGACGTGAATGAAGAACCACAGgtaatttttc ... ttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatatcctcacttcttgttgcatactgtcactcataagcttttttgacctcagGTTGGTGGAGTGTATGTTCGCTTGTTCCTGAAAGATCCCAAATTCCCTCTTCGAAATCCGAAGCGGTTCTTAGAGGGTTTACTTGACCAATATGTCACAG
                                        ctttttt  CT-rich tract
                                         ttttttga  TA-rich tract