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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctcgcccttcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatatatcagctttgcttgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA

Basic information

species Selaginella moellendorffii
transcript EFJ38832
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ38832 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os06g11620.1 (Oryza sativa), 3'ss of exon 3
gtaagtctctcgcccttcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatatat---cagctttgcttgttact-cagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA
            | ||| | |||  ||||     | |  |   |  | | | | || |  || | || | | | |     || | | |   | |||    |  | ||| ||||| || ||  | ||||| || || |||||||||||||||||  | || |||||||| || ||| ||||||| || || |||||||||||||| ||||| |
----------atctcttaatgtttggttttgcatgttgatctttcttatgcttattac--ttagcaatatatgtgccctcaattttttttcctgctgctatgatcactgcagGTTGACTATGCATGCACCCCAGAGGAAGTCCAGCAGCATTTTAATTCCTGTGGAACGGTCAACAGGGTGACAATCCTGACAGACAAGTTTGGGCAACCAA

upper sequence: EFJ38832 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G082198_T01 (Zea mays), 3'ss of exon 3
gtaagtctctcgcccttcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatata-tcagctttg-----cttgttact-cagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA
               |  | |||   ||| | |  || | || || ||  |   ||   | | |||| |    | |  | || |||  |||| || |      | |  ||| ||||| || ||  | |||||||| |||||||| |||||||||||| | |||||||||||||| ||| | ||||| || || || ||||||||||| ||||| |
---------------tcgaagttttatttgtatatatgtctatttgtcagctgtttggttattgaaatatgtaacattacaagtatgctcagtttcggtgtaatggcaactacagGTTGACTATGCATGCACTCCAGAAGAAGTGCAGCAGCATTTCAATTCTTGTGGAACTGTTAACAGAGTGACAATCCTGACTGACAAGTTTGGGCAACCAA

upper sequence: EFJ38832 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G862331_T04 (Zea mays), 3'ss of exon 3
gtaagtctctcgcccttcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatatatcagctttgcttgt-tact-cagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA
         |       ||| | |  | |      |  |||   | ||| ||     |  |    | |  |||  |  |  | |  | | | |    |  | |||| |||||||||||  | ||||| || |||||||| || |||||||||||| ||||||||||||| ||| ||||||| ||  | || |||||||||||||| || |
--------ttaatgggacacatagtttctagccttacatttctgtgtctacccagagcagtcc--acactaagttaacaccatttgaactgatacaatcatgtactgcagGTGGATTATGCTTGCACCCCAGAAGAAGTGCAACAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGACAGCCAA

upper sequence: EFJ38832 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
gtaagtctctcgccct-tcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatatatcagctttgcttgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA
 || |  | | ||    | || |   |  |  || |   |   ||||  || |||||  |  |     |   ||      ||   ||   | | |    ||     ||||| |||||  | ||||| || |||||||| ||||||||||||||| ||||||||||||| ||| ||||||| ||  | || ||||||||||| || || |
-taggcgtgttgcttaatgacataacgcatggtttg---tggccttacatttctgttatccatttgtcagtcagcattttaactgatgcaatcatatactg-----cagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA

upper sequence: EFJ38832 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA15G06030.1 (Glycine max), 3'ss of exon 3
gtaagtctctcgcccttcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatatatcagctttgcttgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA
         | |   || ||    | || |   |    |    || || |     ||   |||    |          | ||    ||    ||    |  | | |||||||| || || |||||||| |||||||| || |||||||| || ||||||||||| || ||| | || || ||||  || || |||||||| ||||| |
--------tttggtgttaacagatacttgcaaacatagtacttttttcatatcactttacttgttgcattgctctcatataatctcatggatttgatgttctccacagGTGGACTATTCATGCACTCCTGAAGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAGTCACCATTCGAACTGATAAGTTTGGCCAACCCA

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: 18 (upstream exon), 32 (downstream exon)
Score: 3

ATGCTAATGCGGCCTCTCAAGCAGGAAAAGAGGAAGCTGATGCTCGCTCCGTCTACGTTGGCAATgtaagtctct ... tgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctttggaaaaaaaagagagaaaaaatatatcagctttgcttgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA
                                      ctttgctt  CT-rich tract
           aaaaaaaagagagaaa  TA-rich tract