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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatgacatactagtgtaggacattggcaagagttttgcatttatgagttgtataatgatcatcagaacgacgttgtccatgcccccttttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA

Basic information

species Physcomitrella patens
transcript PP1S422_18V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S422_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
-------actatgacatactagtgtaggacattggcaagagttttgcatttatgagttgtataatgatcatcagaacgacgttgtccatgcccccttttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA
         ||||| | |||     | |   |  ||     ||||| ||| |   |   ||| ||   ||||| |||  | |||    ||     | ||  |  |||||||||||| | ||||| || ||||| || || || ||||||||||| ||||| || || ||| | ||||||||  |||||||||| ||||| |||||||
tttctttcttatgata-actgaatcaagtt-taagccccccttttggattaacatg--atattattggcatcaaaacccc-ttgaaattgatttgtgtt--ttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA

upper sequence: PP1S422_18V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
----actatgacatactag-tgtaggacattggcaagagttttgcatttatgagttgtataatgatcatcagaacgacgttgtccatgcccccttttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA
    | | |   ||  ||  || |  |  ||        ||||| ||| |   |   ||| ||   | ||| |||  | |||    ||     | ||  |  |||||||||||| | ||||| || ||||| || || || ||||||||||| ||||| || || ||| | ||||||||  |||| ||||| ||||| |||||||
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatg--atattattggcgtcaaaacccc-ttgaaattgatttgtgtt--ttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
















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|67574107|gb|BJ946931.1|BJ946931
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAAT                         GTTGATTATTCCTGCACTCCGGAAG
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAG
EST: gi|208368699|gb|DC940036.1|DC940036
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAAT                         GTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
EST: gi|208366662|gb|DC931319.1|DC931319
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCGAT                         GTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
EST: gi|208389601|gb|DC945825.1|DC945825
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCGAT                         GTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
EST: gi|100400310|gb|BY954413.1|BY954413
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAAT                         GTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
EST: gi|208376819|gb|DC906802.1|DC906802
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAAT                         GTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
EST: gi|162266936|gb|FC441789.1|FC441789
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAAT                         GTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGT
EST: gi|100421243|gb|BY976133.1|BY976133
EST:     CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAAT                         GTTGATTATTCCTGCACTCCGGAAGAGG
genomic: CTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGG

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), 21 (downstream exon)
Score: 8

ATTCTGTGGGCAAAGATGGCTCTCCTGCCAATCGAGAGGAGGCGGATGCTCGCTCAGTTTTTGTCGGCAATgtaaacatat ... ttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttgtataatgatcatcagaacgacgttgtccatgcccccttttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA
                                tccatgcccccttttc  CT-rich tract
       tataatgat  TA-rich tract