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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtataatggaccttgttggtttgttacatggcaaacttcttttattttgattattggattgccaacagaacttgtattttttcttgcaaaaaattaagtactatacctacaacgactgatgtacccactaacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG

Basic information

species Zea mays
transcript GRMZM2G481548_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 6
--gtaatg-tataatg-gaccttgttggtttgttacatggcaaacttcttttattttgattattggattgccaacagaacttgtattttttcttgcaaaaaattaagtactatacc-tacaacgactgatgtacccac-taacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
   ||||  ||  ||  ||  || || |||||||| |||||| | || || ||||||  |   ||       ||   ||||| | | ||     | || |  ||    ||  ||    ||||  |      || |||    | | ||| | |||||||||||||||||||| |||||||| |||||| | ||||||||||| ||||| ||| |||||||||| || ||||| |||
gtataattctaccatctgagttttttagtttgttaaatggcaga-ttattctattttagtacgtg------taatcaaacttat-tattgctaaggaagaggttgttcacgttatggcacaatcatgaggataaccagactatctttgcttcagATTGTAAGGTTCAAAGACAAAGAGTCCCATCAGGTATTTCTTGAACCAGAGGGCAGAGATGTTCCTGAGCTTTATCTGCAG

upper sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G32720.1 (Glycine max), 3'ss of exon 3
gtaatgtataatggaccttgttggtttgttacatggcaaacttcttttattttgat-tattggattgccaacagaacttgtattttttcttgcaaaaaattaagtactatacctacaacgactgatgtacccactaacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
                       || |||| ||    || || | ||  ||||||   ||  |||   ||||   | | | ||  ||| |               | |||   |   | |  |||| ||     |   |  | ||  |||||||||| ||| ||||||||||||||||||| || |||||||||||||||||| ||| ||| ||||| || ||| | |||
-----------------------gtgtgtttca-aaaaagctaccttggttttgaaacatcagat---caactatattggaatcgttttt---------------attat-tttctgatg--tgatatat----tgttcacttttttagATTGTAAGATTCCAAGATAAAGAGTCTCATCAAATATTTCTTGAACCTGAGGGTCGAAGTGTGCCTGAGCTCTATGTGCAG

upper sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 5
-----------------------------------------gtaatgtata-atggaccttgttggttt--gttac-atggcaaacttcttttattttgattattggattgccaacagaacttgtattttttcttgcaaaaaattaagtactat-acctacaacgactgatgtacccactaacccttg--ttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
                                          |||| | |  ||| ||||  ||   |   ||||| ||  ||  |     | |  ||||   |         |  | ||   || |      |   | ||| |  | |   || |  |  |     | |||     |   |   ||   || ||||||||||| ||| ||||||||||||||||||| || |||||||||||||||||| ||||||| ||||| || ||| | |||
gtgtgtttcaaaaaagctaccttggttttcttcatatcagtttaatatgtgtatgtacctgattaactatagttaccatttcattccatactcagattgaacctgaaccatttagaaaaaggggtctgaaacatcagataaactatattggaatcatttgtattattttatgatgtgatatattgttcactttcagATTGTAAGATTCCAAGATAAAGAGTCTCATCAAATATTTCTTGAACCTGAGGGTCGAAATGTGCCTGAGCTCTATGTGCAG

upper sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G13440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtataatggaccttgttggtttgttacatggcaaacttcttttattttgattattggattgccaacagaacttgtattttttcttgcaaaaaattaagtactatacctacaacgactgatgtacccactaacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
                                    |   | | |  | |||  |   ||||      |  | || ||| |   | | |  |   ||| |   |   ||      ||  | |  |||            | ||| |||||||| ||||||||||| |||||||||||||| || || || ||||| |||||  || ||||||||||  | ||| | |||
------------------------------------cttgcatttgctttttctacagttggcacaa-agaataagttgaaccatctttctctttaaactgcttttgatgaacttaaaaaatcttgt-----------ttggtttcagATTGTTAGGTTCAAAGACAAAGAGTCTCATCAAATATTCCTCGAACCAGAGGGCCGAGATGTTCCTGAGATCTATGTGCAG

upper sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 6
gtaatgtataatggaccttgttggtttgttacatggcaaacttcttttattttgattattggatt-gccaacagaacttgtattttttcttgcaaaaaatta-agtactatacctacaacgactga-tgtacccactaacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
                                                   | | ||||   ||| | ||| |||  |    |||||  ||    |  |||| |  |  ||  ||  |  |    |   |      |     | ||| |||||||| || ||  |||||||||||||||||||||| ||||||||||| || ||| ||||||| ||||| || ||| | |||
---------------------------------------------------tggtttataatatttgtcaagagagatgcattttttatttaactatgattacaagaaaatttctgaactgttcaaacatttttttttttggtggtttcagATTGTGAGATTTCAAGATAAAGAGTCTCATCAGATTTTTCTTGAACCAGAAGGTCGAAATGTGCCTGAGCTCTATGTGCAG

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: 45 (upstream exon), 47 (downstream exon)
Score: 37

GACGCACCAAATTGTTATCGACAACTTAGATGAAACACCAACTTATGGTGGTTGGGTTGAAGCGAAGGGACCAAGATACTGCCCGTCAATTGAAGACAAGgtaatgtata ... cttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 35

GACGCACCAAATTGTTATCGACAACTTAGATGAAACACCAACTTATGGTGGTTGGGTTGAAGCGAAGGGACCAAGATACTGCCCGTCAATTGAAGACAAGgtaatgtata ... cttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 32

GACGCACCAAATTGTTATCGACAACTTAGATGAAACACCAACTTATGGTGGTTGGGTTGAAGCGAAGGGACCAAGATACTGCCCGTCAATTGAAGACAAGgtaatgtata ... cttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 17

GACGCACCAAATTGTTATCGACAACTTAGATGAAACACCAACTTATGGTGGTTGGGTTGAAGCGAAGGGACCAAGATACTGCCCGTCAATTGAAGACAAGgtaatgtata ... cttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaattaagtactatacctacaacgactgatgtacccactaacccttgttgcagATTGTAAGGTTCAAAGATAAAGAGTCTCATCAGATCTTTCTTGAACCTGAGGGTAGAAATGTTCCTGAACTATATCTACAG
                                     cactaac  putative branch site (score: 17)
                                           cccttgtt  CT-rich tract
     ttaagta  TA-rich tract