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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggtgttctttttaggacctgcatgcaacgtttatcttgaactatttctggaaaaaaagcatattgaaattggtgatttactgacaatatcatgtgtaatttttcttcgctttgcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG

Basic information

species Physcomitrella patens
transcript PP1S218_133V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 6
--gtttg-tggtgttctttttaggacctgcatgcaacgtttatcttgaactatttctggaaaaaaagcatattgaaattggtgatttactgacaatatcatg--tgtaatttttcttcgctttgcgt----tggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG
   || | |||   |  |||    |      |||||      | ||    | ||| | ||   | || | ||   | |  || | ||| | | | | ||  |  | ||| |||  |     ||| |     | |||||||||||||||| ||  | || |||||  |||||||||| || |||||||||||| | || |||||||||||||| || || || |||
gtattagctggcagtaatttagatatacatttgcaattgacttttttctttcttttttgaggtagag-agatcagagt--gttacttagttaaattgtctcggttctaactttgatgtatcttgtggctaattgcagTGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAG
















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|162279774|gb|FC455682.1|FC455682
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162195316|gb|FC370837.1|FC370837
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162155456|gb|FC330952.1|FC330952
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162260447|gb|FC435060.1|FC435060
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162168819|gb|FC344809.1|FC344809
EST:     TCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: TCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162162467|gb|FC339198.1|FC339198
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208379283|gb|DC927280.1|DC927280
EST:     GTCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162279775|gb|FC455683.1|FC455683
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162173414|gb|FC349793.1|FC349793
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162168239|gb|FC344969.1|FC344969
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208346751|gb|DC917534.1|DC917534
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162246539|gb|FC421128.1|FC421128
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162176625|gb|FC352470.1|FC352470
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|37836927|gb|BJ594935.1|BJ594935
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208353165|gb|DC921867.1|DC921867
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208348181|gb|DC920972.1|DC920972
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208360654|gb|DC946420.1|DC946420
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208395421|gb|DC924475.1|DC924475
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208373658|gb|DC952483.1|DC952483
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|208395675|gb|DC924197.1|DC924197
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|15590637|gb|BI675253.1|BI675253
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162195315|gb|FC370836.1|FC370836
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
EST: gi|162246538|gb|FC421127.1|FC421127
EST:     ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAG                         TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA
genomic: ATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAA

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: 32 (upstream exon), 27 (downstream exon)
Score: 4

CAAAACTTGTGAGGGACGCGTTTCAGTTGGCGAAAGAAAAGGCTCCTTGTATCATTTTCATTGATGAGGTGGATGCTATTGGTACCAAGCGTTTCGACAGgtttgtggtg ... gcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attggtgatttactgacaatatcatgtgtaatttttcttcgctttgcgttggcagTGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG
          tactgac  putative branch site (score: 4)
                               tttttcttcgctttgc  putative PPT
                            taatttttctt  TA-rich tract