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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG

Basic information

species Zea mays
transcript GRMZM2G064831_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttt-tgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                                                ||| ||  | | ||||   | |  |  |  | | |||         | |    |  ||||||| | || ||||| || |||||| | |||| || ||||||| |||||||  | | |||| |||||||| || || ||||| || |||||||||||||||||||| ||||| || ||||| |||||||| ||||| |||||||||||||||||||||||  ||||||
---------------------------------------------------------------gtaatttcctaatatttacctgttcattaaaattcata--------gggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG

upper sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                                           || | |||||    | |||  | |||  |    || | |   | ||  || |      | |  |  |  ||      | |   |||    |||  | ||  |  ||  |  |||   |||  ||  | |||||| |||| ||||| || |||||| |||| || ||||| ||||| || ||| |||| || |||||||| ||||||||||| ||||||||||| ||  | |
-----------------------------------------------------------gtaagtaactc--aagattgatatcttgatttgtagttaagca-gtaccaaagcatgcataggttcagtgtt----tagtctgttgtatagtagtgttatttttttaattcctttttctgt-tgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG

upper sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                              |    | ||| |  |  ||| ||      ||||  |  | |   |  ||  |   |||  |    | |  | |  || | ||    |   | ||  ||| ||  | |   | | |||||||||| ||    |         |||||| |||| ||||| || |||||  |||| |||||||| ||||| || ||| | || || |||||||| ||||||||||| |||||||||||  |  | |
---------------------------------------------gtgaggaagttaagattgatatctca----attttgtagttaggcagaaccaaagcatgcat----aggtttgatgtttagtctgttatatagta--ttgttatttta--ttgattcatttttctgttgtttt---------cagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG

upper sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                                                                    |  |||| || |  | | | ||  ||      || |  ||| |  |        | ||||       | | ||   || || ||   || |      ||  | |||||| |||| || || || |||||| |||| |||||||| ||||| || ||  | || ||||||||||| || |||||||||||||||||||  ||  | |
------------------------------------------------------------------------------------tgcaaaattaatattttttcttcaagttgttatacacatcatttattttgattttgcttt------cagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG

upper sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcag---aaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                                                                             | ||||  ||| |  |     | |  |  ||     || ||  || ||   || || | | |   |     | || ||   || |      ||  | |||||| |||| |||||||| |||||| |||| |||||||| ||||| || ||| | || ||||||||||| || |||||||||||||||||||  ||  | |
--------------------------------------------------------------------------------------------cattgatgcatgctgaaatttgatgtttttatgctgttc-tatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG

upper sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                                                              ||| | | |   | | ||  | ||   |   |  || | |  ||  | || ||   | |  | ||      |  |  |||  | ||| |  | ||    |       |||||||||| || ||||| || |||||| | || |||||||| ||||| ||||| || |||||||||||||| ||||||||||||||||||||||   |  | |
------------------------------------------------------------------------------tgtcttttagggatt-ctattttacaat---ggtagtccaggttaaagtcctatgtgaaggaattca----gagagagtacttgattgtgattttctattttt----tgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG

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 4 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 39 (downstream exon)
Score: 7

CACTGAAATGAATGATGGTGTTTTGAAGGACAAGCAACTTTCGACTAAGGAGATTGCAACTTATGGATTGTATCTTTGCCCCTTATGGTTTGTGACAGAGgtaattttac ... atgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG


Block sizes: 42 (upstream exon), 8 (downstream exon)
Score: 3

CACTGAAATGAATGATGGTGTTTTGAAGGACAAGCAACTTTCGACTAAGGAGATTGCAACTTATGGATTGTATCTTTGCCCCTTATGGTTTGTGACAGAGgtaattttac ... atgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG


Block sizes: 13 (upstream exon), 49 (downstream exon)
Score: 3

CACTGAAATGAATGATGGTGTTTTGAAGGACAAGCAACTTTCGACTAAGGAGATTGCAACTTATGGATTGTATCTTTGCCCCTTATGGTTTGTGACAGAGgtaattttac ... atgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

CACTGAAATGAATGATGGTGTTTTGAAGGACAAGCAACTTTCGACTAAGGAGATTGCAACTTATGGATTGTATCTTTGCCCCTTATGGTTTGTGACAGAGgtaattttac ... atgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
                                 ctcttac  putative branch site (score: 161)
                         tcattttt  TA-rich tract