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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA

Basic information

species Zea mays
transcript GRMZM2G062034_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g13580.1 (Oryza sativa), 3'ss of exon 11
------------------------------gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtact-cataaaatagcactgagt----tatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                               | ||  ||   ||  | | ||  |||  | |    ||| |  |   |||   |  ||  | |  ||   |||  | ||  |    |||||||   || || ||||  ||||  ||  ||   ||||||   || ||||| || || | |||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||| |
gtacatgataagtggtcagtacaacttaatcttctgttgggtttccattgaagctattgcatcaaattagttcaacaaatccttcaaaaaattatatcccataatagtgtatgtcatatacatcaattctcttatccctcttattttgtta--atagATGCTGTCTTCAAGGACATACAGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTCTGCATTTTCGCATATGGGCAAACTGGATCAGGAAAAACATA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactca--taaaatagcactgagttatacattttttgtcatatctttctttc-ttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                         |  | ||  | ||||| | ||| ||  |  |   | |     |||  |   |       || |   | ||||  ||    | ||   |||  |  |  ||    ||| | |   || ||||   |  | || ||||||||||| ||||| || ||||| || || ||||| ||||| |||||||| ||||| |||||  |
-------------------------aggttttaggattaattttttttatcacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
-------gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagtt--ata-cattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
       ||  |  |  | ||    |   |  ||   | || ||  ||   | | |||  |||  |||||  |    ||    |||  |  |||  | | |||  | ||| | ||  | || ||  || ||||     | ||||| || | ||  ||| | ||| |||| ||||||||||| ||||||||||| || ||||| |||||||||||||| || ||||| ||| |
gtactgcgtttttttttcttttctctttcatgattattattatt--attattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 13
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatt-taattgctataagtactcataaaatagcactgagtt--ata-cattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
              | | |  |  | | | | || | || |  ||  | |||  ||| ||||||  |    ||    |||  |  |||  | | ||   | |||   ||  | || ||  || |||      | ||||| || | ||  ||| | ||| |||| ||||||||||| ||||||||||| || ||||| ||||||||||| || || ||||| ||| |
--------------gtactgcatttttttttcttttctatttcatgattattattattagtacttgttttctattgttgaaattgatagtaatgttcaacttatacatcaatatttttctttgtagGGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 11
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgt----tatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                            | ||  | ||||| | |||||      |     ||  |  | | |   |  ||||  | | |  |||  ||    |  |  |   |||     |  ||    ||| | |   || ||||   |  | || ||||||||||| ||||| || ||||| || || ||||| ||||| |||||||| ||||| |||||  |
---------------------------gttttaagattaatttttttaacacagtttctcccttttttagttgt--tatgttaaccttctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------gtgcta-atgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtac---tcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                       || || ||  | ||    |    |  | | |||||| | ||||||   |    |    ||||   ||   |||||  | |   ||  | ||          || |    || | | || ||  || |   || ||    || ||  | || ||  |||| ||||| |||||||| ||||||||||| || ||||||||||| || || |||||||| |||||  |
gtgtgttcatctgttaccggttctgttatatatccttatgcttttcagttctgttttgtgtgatctatgcgagaattcatggtacatctcgagaaataatattatattg-atatcaccaagttcatttgatattttggattcttgcagCTGACGTCTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 13
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttc-tttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                                  |||||| |   ||     || || ||| |  ||   |    ||   | ||| ||  | | ||||||| |   | | || | |  | ||||   |||||||   |||| ||| ||| ||||| ||||  ||||||||||||| |||||||| || ||||| |||||||| ||||| || ||||||||  |
----------------------------------gtttaaacctctttccctct-tatgtattgttagcgttttcctctataatatatgatat-tcatatcctgaatctgttatcttatgtagAGGAGGTTTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
||| |  |    |||    |  ||| | ||||   | ||  || |||  | | |    ||  || |   |     |  |   ||  || |  |    |   | | | | ||  || ||  || |  ||| ||    |||||    || || ||| ||||||||||||| || |||||||| || || |||||||||||||| || |||||||| |||||  |
gtgttcttttgtttgcctgaggaatttttcttcaatata--ctttttgttggattggtgtgttcttgggactaatcaaaaaaattaatatacttatgtcattgtatcttttaattcttgcagCTGAGGTATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 12
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                  |    ||   | | || | |||| |   |  |||     |   ||   || | | ||     |||||    ||   ||||||  | |||      |  || ||| |  ||| ||    || | ||  ||  |  |  |||| |||||||||||||| ||||| || || ||||| |||||||||||||| || || || ||| |
----------------gtttttcatccttatattttataatttggatccttgaatagatctctttcaagaaatca-----ttataatgcttgactcatattatgcttggaaaatgtttgtagCTGAGGTGTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 14
-----gtgctaatgacattgaa-ataaaaatatatcttttgtttaatctattt---aattgctata------agtactcataaaatagcactgagttatacattttttgtcat-atctttctttcttgtttgttat-agATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
      | || || | |||  | ||       | | | ||  ||  | |||      ||| ||||       || |  | |    ||| |  ||  | |  | ||  |  | | || | | | |    | |||||| |||   ||| ||    || | ||  ||| ||||| |||| || |||||||| |||||||| || || ||||| |||||||||||||| || ||||||||  |
gttatcttcttataatattttatatttggccttgtttctttatttgtatatcctcagatttctattccacttagcatgcttttgttaggaaagaacttttaacttactacctttatttgtatatacattgtgttatcagAGGAGGTATTTTTAGACACTCAACCATTAATTCGATCTGTACTTGATGGATACAATGTCTGTATATTTGCCTATGGTCAAACTGGCTCTGGAAAAACCTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ19920 (Selaginella moellendorffii), 3'ss of exon 8
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                                                                 ||  | |||  |  |||| |    | |||   |||     |    ||||||    |||    || |||   |||| || |||| | ||  | |||||||||||||| ||||| || || |||||||| ||||||||||| || || ||||||||  |
----------------------------------------------------------------gtagtaaagc-ttccgttaaag---tcttgatgtataaacttgatatgtttgc---agAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

upper sequence: GRMZM2G062034_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ12333 (Selaginella moellendorffii), 3'ss of exon 8
gtgctaatgacattgaaataaaaatatatcttttgtttaatctatttaattgctataagtactcataaaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                                                                 ||  | |||  |  |||| |   ||  |||   | ||| || | ||      |  |||    || |||   |||| || |||| | ||  | |||||||||||||| ||||| || || |||||||| ||||||||||| || || ||||||||  |
----------------------------------------------------------------gtagtaaagc-ttccgttaaagtcttgatgtagaaacttgctatgtt------tgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

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: 47 (upstream exon), 46 (downstream exon)
Score: 52

GAGAATGGTGAACTGGTTTTATCAAACCCTACAAAGAAGGGAAAGGAAGCCGGCAAGAATTTCACTTTTAACAAGGTTTTTGGCCCTACAGCTACACAAGgtgctaatga ... tttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 20

GAGAATGGTGAACTGGTTTTATCAAACCCTACAAAGAAGGGAAAGGAAGCCGGCAAGAATTTCACTTTTAACAAGGTTTTTGGCCCTACAGCTACACAAGgtgctaatga ... tttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA


Block sizes: 47 (upstream exon), 12 (downstream exon)
Score: 9

GAGAATGGTGAACTGGTTTTATCAAACCCTACAAAGAAGGGAAAGGAAGCCGGCAAGAATTTCACTTTTAACAAGGTTTTTGGCCCTACAGCTACACAAGgtgctaatga ... tttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 37

GAGAATGGTGAACTGGTTTTATCAAACCCTACAAAGAAGGGAAAGGAAGCCGGCAAGAATTTCACTTTTAACAAGGTTTTTGGCCCTACAGCTACACAAGgtgctaatga ... tttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatagcactgagttatacattttttgtcatatctttctttcttgtttgttatagATATGGTTTTCAACGATATTCGGCCACTAATTAGATCAGTTCTTGATGGCTACAATGTTTGCATTTTTGCATATGGTCAAACTGGATCAGGAAAAACACA
                    ttttttgtcatatctt  CT-rich tract
           agttatacatttttt  TA-rich tract