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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactactaacttcctatttcaatgagaactatattatgctagttgatgtgaatggcgtaaaagcactagaaagccatcggtagaatttgctcgacatagttctggtataacagcatgtgttgatagaggtggaagttgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCA

Basic information

species Physcomitrella patens
transcript PP1S61_267V6.1
intron # 2
splice site 3'
intron type U2

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|208384519|gb|DC914991.1|DC914991
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|18368471|gb|BJ200556.1|BJ200556
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|18369302|gb|BJ201388.1|BJ201388
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|7147997|gb|AW509919.1|AW509919
EST:     TAGCTAAGCAGACGCCTTTATGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|208363576|gb|DC939767.1|DC939767
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|208357429|gb|DC910742.1|DC910742
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|162152018|gb|FC328439.1|FC328439
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|18375207|gb|BJ206785.1|BJ206785
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|162258565|gb|FC434780.1|FC434780
EST:     GCTAAGCAGACGCTTTTAGGGTTTAC-AGCCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: GCTAAGCAGACGCCTTTAGGG-TTACAAG-CCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|162258566|gb|FC434781.1|FC434781
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
EST: gi|100431663|gb|BY960311.1|BY960311
EST:     TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAG                         GGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG
genomic: TAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTG

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), 29 (downstream exon)
Score: 15

GGAGCACTGCCTGTGCCATTTGGCCACGGGCGACATGCTGCGCGCAGCGGTAGCTAAGCAGACGCCTTTAGGGTTACAAGCCAAGGCTGCTATGGACCAGgttactacta ... tgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacatagttctggtataacagcatgtgttgatagaggtggaagttgattggcagGGCGCGCTGGTTTCCGATGACTTAGTGGTAGGAATTATCGAGGAGGCTTTGAAACGGCCGTCATGTTCAAAGGGTTTTATTCTTGATGGCTTCCCCCGCA
              tataaca  TA-rich tract