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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA

Basic information

species Zea mays
transcript GRMZM2G047860_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
|||||||| |  |||||||| | |  | | | ||    |||  |  | |   || ||         | || |||||| | ||   | || ||  ||| |||| | ||||||||||| ||||| ||||| ||||| ||||||  |||||| ||||||||||| |||||||||||||||||| |||||||||||||||||||||||||||| 
gtaagtattat-tttgttgtaattcaatattttgccattttgattgtttgattatttc--------tgttattatatatatatatatttact--tttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G10730.1 (Glycine max), 3'ss of exon 2
------------------------------gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagc----agtattgtta------tatttctaaccactttctgttttggcacctt--tgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
                               ||  ||     | |||| ||  |  |   ||  |  |  |||    | |  | || || |||     | |||||| |      ||||| | |    | |  ||||| |     |  ||||||||||||||  |||| || || ||||  ||   |||  | |||||||||||||||||||||||||||||  | ||||| || |||||  | ||||| || 
gtaagtgcaatcttaatcttcctcgtttccttacatacactatgtgtttttgttgaatgttccatctgcatttattccattgtcctgtgagaggtcaaattattgtgactgatttattttttattgatgtgggttttcgtgttgtgctgcagATATGCTTCAATTAGGGCGATTGAGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTT

upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G01160.1 (Glycine max), 3'ss of exon 2
------------gtaagtatcacctttgttgttaattgacagtctgtag-gttttttcctcttgatactttgtgagcagtattg---ttatatttctaaccactttctgttttggcacctt--tgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
             | |   ||  ||||    |  |   ||| | |||   |||   |  || |  | | ||     || | |||   | ||   | | |    | |  ||||| |    ||  | ||||||||||||  |||| || || ||||  ||   |||| | |||||||||||||||||||||||||||||  | ||||| || |||||  | ||||| || 
gtaagcaaaatcttgatcttcctcttttccttacacgcacaatgtgttttgttgaatgttccttttgcatttattccattgttggactcattcatattattgatgtgggttttcgtgttttgcttcagATATGCTTCAATTAGGGCAATTGAGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtatcacctttgttgt-taattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttg-cagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
        ||  | |||| | ||||     || || | |||| |   | ||  |  | || ||| |   |  ||  |  | |      ||  ||   |||   ||||| ||||||||| ||  |||| || || ||||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  | |||||  | || ||||| 
--------catgtatgttctataatatgtggtttgaatgtttgt--gttttagttttctgagagaaaattgcttgaaacttttgtt--ttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

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|211371979|gb|FL186724.1|FL186724
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|32808662|gb|CD960896.1|CD960896
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|47961761|gb|CN844470.1|CN844470
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211371978|gb|FL186723.1|FL186723
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|94472096|gb|EB701054.1|EB701054
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|76014693|gb|DT941863.1|DT941863
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|86465815|gb|DY232188.1|DY232188
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA

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), 47 (downstream exon)
Score: 232

GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 111

GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 211

GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 99

GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
                      ttctaac  putative branch site (score: 99)
                                            caccttt  putative PPT
           tattgttatatttcta  TA-rich tract