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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
------------------gttcgtatttatttgagatta--atcgattcatt--ttatatatctgtttcaacatcaaatga--tttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
                     |||| |    |   ||    |   ||| | |  || ||||||||     |   | | | |   ||  |||||||  |||||||   |||||||||||| || ||||| || |||||||||||||| || ||||| || |||||||||||||| |||| | |||| || ||||
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------gttcgtatttatttg-agattaatcgattcat-tttatatatctgtt-tcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
                                                 |   ||| ||| |  | ||  ||  ||  || | ||||||| ||   |||  || |  |||| || | | ||| ||||| ||  ||||||||||||| ||||||||||| ||||| ||||| || || ||||| || || ||||||||||| |||| | |||| |||||||
gtatgcattttgcatgagatactctgactattaagtaattatatatatatatatatatatatatatatatatatatatatatatatatatatgccatcattattagctgatatgctgtgtaacacatgtatt-ttgtagGACGTGGAGCTAAGGAAGCCAATCTCTACACCGAGATAGCTGAAGGCATTCATGCTTATGGAATAAAAGGCCACCGGCATG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
gttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
           |||||| ||| ||  |      |  | |  || | |||  |    |  |||  |  || | |      |      ||||||||| |||||||| |||||||||||| |||| || ||||| || ||   | |||||||  | ||  | ||||| ||||
----------gtttgagcttactccgtgatcaatgaacaa-tgatgcaatgtttc-tagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
----------gttcgtatttatttgagat-taatcgatt--cattttatatatctgtttcaacatcaaatg-attt----ggtctctaaaacatgcatcatt--gtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
           ||  | |||||||   ||  ||    ||  || | |||||   || ||| || |  |    ||||     |  | |   |  ||   ||||  | ||| ||||| || ||||| |||||||| ||||||||||| ||||| || || ||| ||||||| || ||||| ||||| ||||
gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG

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|31354246|gb|CD438603.1|CD438603
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|74234670|gb|DT642584.1|DT642584
EST:     CAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATC
genomic: CAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGT-GGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATC
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAG-GGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC

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: 246

GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 112

GCAAAACTGATCAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
                                ctctaaa  putative branch site (score: 112)
                    aaatgattt  TA-rich tract