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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgttgccgtcaataagtggcgaatttagataactaatgagagaccgttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ14095
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GRMZM2G045821_T01 (Zea mays), 3'ss of exon 10
--------gtgctgttgccgtcaataagtggcga-atttag---ataact--aatga---gagaccgttttccttc--------acagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
          | |||  || ||| |   |    | |||||    ||||    ||||     | ||  ||||  |          | ||||||||||||||| |||||||| ||||||||||| |||||||| |||||||| ||||||||||| |||||||||
gttagttctcgatgtgtccttcattgcattttaagatttattttataatctgaatgtcctaaaactctttttttgtgtggaaatatagGCACTGTGGTGGACTCGAAGATCTGCCATCCAACTGAGTTTGATTTCTACCTGTGCAGCCATGCTGGCATTCAG

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 18
---------------------------------gtgctgttgccgtcaataagtggcgaatt-tagataactaatgagagacc----gttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
                                  |    |||  | ||| | ||  |    |  |  |  ||  |||  |  |    |||       ||||| || || || ||||| ||||| ||||| |||||||||||||| |||||||| || || ||||| || || |||
gaggcagccagatttttcttttgtttaaatcgcattacattgaag-caagatgtaacaccctacatttttcttttgactgctcacaagttgattgaaacagGAACCGTTGTTGATTCTAAGATATGCCACCCAACGGAGTTTGATTTCTACCTCTGTAGTCATGCTGGAATCCAG

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 16
----------------------------------------------------gtgctgttgccgtcaataagtggcgaattt--agat--aactaatgagagaccgttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
                                                    |      || | ||| |  |   |   |||  ||||  | ||||  | |    ||| |  | ||||||||| ||||| ||||| || ||||||||||| || || ||||| || || || ||||||||||| || ||||||
gtaaagtttttgtttcatggaaaaatacaatttttgctgtgtgcatatgtatggaaacatgtcctcactggggttcctttttccagatttatctaaccatatttggttcttttccacagGCACAGTGGTTGATTCTAAAATTTGCCATCCGACTGAATTTGATTTTTATCTCTGCAGCCATGCTGGTATTCAG

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------------gtgctgttgccgtcaataagtggcgaatttagataactaatgaga-------gaccgt----tttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
                                                      |  | ||||   ||||  | |  | | | ||||  |  |||  |         | | |    || |  |   ||| |||||||| ||||||||||| |||||||| |  ||||||||||| || || ||||| ||||| || || |||
gtaatattttcttacttataattttatttagattatgtcttgatggttgagcttgatccgttg--atcaaacaatctccactctagaatagcaatacggttgttacaagcatgaagttcctattgtagGTACTGTGGTCGATTCGAAGATCTGCCATCCCAGTGAGTTTGACTTTTATCTATGCAGTCATGCAGGAATCCAG

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------------------------------------------------------------------------------------gtgctgttgc---cgtca--ataagtggcgaatttaga-taactaa-tgagagaccgttttcct----tcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
                                                                                                ||| |||||    |||     |||    ||  |||| | | ||||| |  || | |   | | |    |   ||| ||||| ||||| ||||||||||| || || |||||||||||||| || |||||||| ||||| || ||||||
gtgcagtcattattttcgtagaatacattgctttatttatctgcttatatggaagtcattttctttggcattctcaacctgtgagactgcggtatggtgttgttggacgcgttgctgtaacaaccgtgtttacactgactaacttcgacatcacatccttcgtattttagGGACTGTTGTGGACTCGAAGATTTGTCACCCTACGGAGTTTGACTTTTATCTTTGCAGTCATGCTGGAATTCAG

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|169025753|gb|FE433663.1|FE433663
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169052412|gb|FE462246.1|FE462246
EST:     CGATCACGACGATACAAGAACTACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169094763|gb|FE492940.1|FE492940
EST:     CGATCACGACGATACAAGAACTACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169110846|gb|FE509329.1|FE509329
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169036142|gb|FE445663.1|FE445663
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169053756|gb|FE461523.1|FE461523
EST:     CGATCACGACGATACAAGAACCATTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169076999|gb|FE485340.1|FE485340
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169081815|gb|FE486414.1|FE486414
EST:     CGATCACGACGATACAAGAACCATTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169026881|gb|FE432386.1|FE432386
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169078633|gb|FE487065.1|FE487065
EST:     CGATCACGACGATACAAGAACTACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169108088|gb|FE511031.1|FE511031
EST:     CGATCACGACGATACAAGAACCATTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169026857|gb|FE434221.1|FE434221
EST:     CGATCACGACGATACAAGAACCATTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169076998|gb|FE485339.1|FE485339
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169027233|gb|FE435091.1|FE435091
EST:     CGATCACGACGATACAAGAACTACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169026895|gb|FE432387.1|FE432387
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169092972|gb|FE495266.1|FE495266
EST:     CGATCACGACGATACAAGAACTACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169021773|gb|FE430420.1|FE430420
EST:     CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
EST: gi|169077159|gb|FE484538.1|FE484538
EST:     CGATCACGACGATACAAGAACTACTGATAAGAGTGGAAATATCCTGCCAG                         GCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC
genomic: CGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACC

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), 35 (downstream exon)
Score: 44

GTGACGTTCGTTGTGGTCCAGAAACGGCACCACACCCGGCTATTTGCTAACGATCACGACGATACAAGAACCACTGATAAGAGTGGAAATATCCTGCCAGgtgctgttgc ... tccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgtcaataagtggcgaatttagataactaatgagagaccgttttccttcacagGCACTGTGGTGGATTCGAAGATTTGCCATCCAACGGAGTTTGACTTCTACCTTTGCAGCCATGCCGGCATTCAG
                          aactaat  putative branch site (score: 44)
                                       ccgttttccttcac  putative PPT
                 aatttagataactaat  TA-rich tract