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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 7
gtaggcttctcttg-ccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
|||||  || | || |     | | |||||  |   |            |  ||| || | |||   || ||   || | | || |    |  || | || || |  |||  | |  |  | ||||| | || |     ||||||||||||||||||||| ||| |||||||||| |||||| | |||||||||||||||||||| || || |||||||||||||||||||| ||||| ||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggt-ttacatcctcaagcatttttt----tgcttttattctgat--aattcgttgatgctatgatt-gatgttt----gcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 7
gtaggcttctcttg-ccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
|||||  || | || |     | | |||||  |   |            |  ||| || | |||     |||   || | | || |    |  || | || || |  |||  | |  |  | ||||| | || |     ||||||||||||||||||||| ||| |||||||||| |||||| | |||||||||||||||||||| || || |||||||||||||||||||| ||||| ||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacattcctcaagcatttttt----tgcttttattctgat--aattcgttgatgctatgatt-gatgttt----gcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 7
----gtaggcttc-tcttgccactatttgtttttat-ataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaa------tctgatcctagtctgatttgct--gctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
    ||  ||  |  |||| |||  |   | |  ||    |    ||||  |     | |  ||    |   | |   ||||   || |     |||  | | ||   ||| ||      ||  ||  ||     | |  ||    ||    |||||||||||| ||||| || ||| |||| ||||| |||||| | |||||||||||||||||||| ||||| |||||||| ||||| ||||| || |||||||
gtatgttagcaccaccttgtcacattaattctacattgctacctatgcaaattttgtactctttctaatctaattatggtaatt-tgcttcagtatacatttcttcaagttcaagttatgtccaattttatcaccactgacttgattatgctgcagAATAATCTTCATGAACTTTGGTCTCTTCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAGACTTTTGATGATTGGTTCCAAATCTCAGGGGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 7
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                      || |||| ||   ||        || ||   | |||    |     ||   |    || |    ||  |  |||||  | ||    |||  |   | | | ||| ||          |||||||| || ||||| |||||| |||| ||||| ||  | || || ||||| ||||| ||||| || || |||||||||||||||||||| ||||| ||||
----------------------tgcttttctaccttgt-----tttgaaatcttaatt---attttttttgtttgtttgtatgcatcctcaaatatttactagt---gtctattatcacttttattggc---------acagAATAACCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatc-ctagtctgatttgctgct----acatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                                             | |||   ||| ||   | ||  |||| |    |  | |     |  | || ||    |  | |    |   || | ||||||| | ||    || | |||||| ||||| ||||| ||||||||||| ||||| ||  |  | |||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||
---------------------------------------------ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgtt--aatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 7
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatc-ctagtctgatttgctgct----acatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                                             || ||     || |   | ||  |||| |    |  | |||  |    || | ||   |  | |    |   || | ||||||| | ||    | || |||||| ||||| || || ||||||||||| ||||| ||  |  | |||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||
---------------------------------------------tgaaatctgaatcttatttccctttcattggttgcat-gtgtaagcgataatgtt-aatacacttaagtaattaatgtgatttgtttcttttgatattgcagAACAATCTTCACGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 7
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgccatatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                                       |||   |  | |  | |||| |  | |    |  | |   | ||||    |||  ||  |    | |   ||| |    || | || |  | | |     ||||||||||| ||||| |||||| |||| ||||| ||  | || || ||||| ||||| ||||| || || |||||||||||||||||||| ||||| ||||
-------------------------------------tatgcttttctagc--ttattttgaaatctgaactattatttttttgt-ttgtatgcatcctcaaatatttactggtgt--gtattatctctttcaatggcacagAATAATCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------gtaggcttctcttgcca--ctatttgtttttatataatgcgtgcacctggaaca-atgatttaggtaccact-tcagtaaccgtgttgt--gccatatttattttttggtttaatctgatcct--agtctgatttgctgcta-------catg---gcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                                      | | ||   |||  |   |  || |  ||  ||  ||     ||||       | |  |  | |  |||| | |      |  ||    | ||  |||| | |||    ||   |||   |  || ||| | | ||  ||       |||    |||||||||||||||||| || |||||||| || |||||  | || ||||| || ||||| || || ||||| |||||||||||||||||||| ||||| || |
gtgtttgctctatcttattcttgaatatttggacattgaagttttctttgttaagttgcttctaattgaatgttgaaacaacctttcttgtacggctctgtttgcactcttaacttttgcttttccgggcacttttaatatttaccgtataatgactgtgtagcctgctgtactcatattgtcctcatatatgcagAATAATCTCCATGAACTGTGGGCTCTTCTAAATTTTCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 7
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgt-tgtgccatatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                                                             |||| |      ||   |||   ||||  ||||||||||    |||   ||  |  |   |  ||||     || |   ||||| || || || ||||| ||||| ||| | |||||  | || || ||||| ||||||||||| ||||||||||| || |||||||| || ||||| ||||
-------------------------------------------------------------gtacaa----gatagttgtgaacgtgct-tatttattttaccctttttccttgtttt---cccattt----ttataccacagAACAACCTGCACGAGCTGTGGGCGCTCTTGAATTTTCTCCTGCCCGAAATCTTTAGCTCTGCTGAGACCTTTGACGAGTGGTTTCAGATTTCTGGAGAAA

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 7
gtaggcttctcttgccactatttgtttttatataatgcgtgcacctggaacaatgatttaggtaccacttcagtaaccgtgttgtgc-catatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                                                                          ||    ||||||  | |  ||||||| |  |||| |||  | |     |       |  || |   ||||| || || || ||||| ||||| ||| | |||||  | || || ||||| ||||||||||| ||||||||||| || |||||||| || ||||| ||||
----------------------------------------------------------------------gtacaagatagttgtgaacgtgcttattttat--tttactctttttccttgttttcccatttttataccacagAACAACCTGCACGAGCTGTGGGCGCTCTTGAATTTTCTCCTGCCCGAAATCTTTAGCTCTGCTGAGACCTTTGACGAGTGGTTTCAGATTTCTGGAGAAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 470

TGAAGCTCACCGGATAAAAAATGAAAATTCTCTTCTATCAAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

TGAAGCTCACCGGATAAAAAATGAAAATTCTCTTCTATCAAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

TGAAGCTCACCGGATAAAAAATGAAAATTCTCTTCTATCAAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

TGAAGCTCACCGGATAAAAAATGAAAATTCTCTTCTATCAAAGACTATGAGGATTTACAACACTAATTATCGTCTCCTCATCACAGGCACTCCACTCCAGgtaggcttct ... tacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttattttttggtttaatctgatcctagtctgatttgctgctacatggcagAATAATCTCCATGAGCTCTGGGCTCTCCTCAATTTCTTGCTACCTGAAATATTTAGCTCTGCGGAGACCTTTGATGAATGGTTTCAAATATCTGGGGAAA
                               gtctgat  putative branch site (score: 164)
     ttattttttggtttaa  TA-rich tract