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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtgaaggatttttgtcattctacattgtatgtagttaattgttttccaaatgtgcgggtggctctgcatgttgatattgtatatgattgggta...

Basic information

species Physcomitrella patens
transcript PP1S218_133V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S218_133V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 7
TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtgaaggatttttgtcat-tctacattgtatgtagttaattgttttccaaatgtg---cgggtggctctgcatg-ttgatattgtatatgattgggta
|||||||||||| ||  | || |||||  |||||||||| || |||||||||||| | || |||||||||||||| || || || |||||  |   | ||   || |||| || | ||  || | | |  || |   || |  || | ||   | |     | ||| |  ||    |     || || |  | 
TGAAGTAAGTGGAGACAGAGAGGTACAACGAACTATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATCAAGgtttgtctttaa---ttcttgttatctatatgttttttctgattgac-attatataagtatgcttcagagaattttgctttctttgggtaaagcataatagttt-
















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:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162195316|gb|FC370837.1|FC370837
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162155456|gb|FC330952.1|FC330952
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162260447|gb|FC435060.1|FC435060
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162168819|gb|FC344809.1|FC344809
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162162467|gb|FC339198.1|FC339198
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208379283|gb|DC927280.1|DC927280
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162173414|gb|FC349793.1|FC349793
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162168239|gb|FC344969.1|FC344969
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208346751|gb|DC917534.1|DC917534
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162246539|gb|FC421128.1|FC421128
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162176625|gb|FC352470.1|FC352470
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|37836927|gb|BJ594935.1|BJ594935
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208353165|gb|DC921867.1|DC921867
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208348181|gb|DC920972.1|DC920972
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208360654|gb|DC946420.1|DC946420
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208395421|gb|DC924475.1|DC924475
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208373658|gb|DC952483.1|DC952483
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|208395675|gb|DC924197.1|DC924197
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|15590637|gb|BI675253.1|BI675253
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162195315|gb|FC370836.1|FC370836
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
EST: gi|162246538|gb|FC421127.1|FC421127
EST:     TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAG                         GTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT
genomic: TGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGT

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: 15

TGAAGTAAGTGGTGATCGTGAAGTACAGAGAACTATGTTGGAGTTGCTTAATCAGTTGGACGGTTTTAGCAGTGACGAGCGCATAAAGgtgagctgtg ... ccatgaacagGTAATAGCAGCTACAAACAGAGCAGATATTTTGGACCCTGCTTTGATGCGTTCTGGACGTTTGGATAGGAAGATTGAGTTTCCTCATCCAACGGAGGAGG




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