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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgcacagttctttctattacccctcctgcactataatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatcatgtgatgtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA

Basic information

species Zea mays
transcript GRMZM2G063792_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
gtgtgtgcacagttctttctattacccctcct---gcacta--taatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatc--atgtgat------gtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA
||||||||||||||| |||| |||| | |  |    |||||  ||    || || |||| | ||    |   |   |||||   | |||    |   | || | ||  |     |  | ||    ||| || |||| | |  |  || |      |||| | |||||| | ||||| |    |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcat-cagttgatagctgatgctttctttgc-ttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgtgcacagttctttctattacccctcctgcactataatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatcatg-tgatgtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA
                                                                               |  |  || |  ||| | | |   |     ||    |  |   ||  | |  |||  ||    ||||  || | ||      | |   ||||   |||||||||||||||| || ||||||||||| || ||||| ||||||||||| || || || || ||||| || ||  ||||||| || || ||||| 
------------------------------------------------------------------------------ctttaaactttgtttactgcttgcattggattttggatttaattagggttt--cattgtgactctgttgctgaagttgggtggttttgataatactttgcagTTATGCATGATTTACGCCTCATACATACGGATTTGAAGCCTGAGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG

upper sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgtgcacagttctttctattacccctcctgcactataatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatcatgtgatgtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA
                                                                              ||      |   | ||||       |   | | | |       |  ||| |   ||| |     ||  |  | || ||  |  | || |||    ||||||| |||||||| |||| |||||| |||||||| || |||||||||||||| ||  |||||||||| || ||  | |||||  | || ||||| 
-----------------------------------------------------------------------------tttatgaaataaaaataatatggagtttgagat-ggataattttgtttatttgctatcctacagagtgctaatgttgactttgac-ctataaaaatttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATACTTTTTGTTTCTCCAGAATATGTAAAAGTATCAGACTACAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|7162469|gb|AW520091.1|AW520091
EST:     AATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCAT                         TTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTC
genomic: AATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTC




















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: 48 (upstream exon), 48 (downstream exon)
Score: 158

GGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 135

GGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 157

GGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 178

GGACCAAGCTTATATGATTTTCTGAGGAAAAACAATTACCGCTCATTCCCAATTGCCCTAGTTCGGGAGTTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctaacatcatgtgatgtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA
 atctaac  putative branch site (score: 178)
                atgtttttgtattta  TA-rich tract