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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcgttatcactttttttatcttgagtggttcccccttctttaagcagtttatcttttgtcattgtaaccaatgtctaccttttctcattcag

Basic information

species Zea mays
transcript GRMZM5G825110_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 11
ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcgttatcactttttttatcttgagtggttcccccttctttaagcagtttatcttttgtcattgtaac-caatgtctaccttttctcattcag
|||||||||||||| |||||||||||||| ||||| ||||||||  | || || |||| |||||||||| |||||||||| ||||| |||| | |     |||  |||     |||      ||  ||   ||      || |||| ||| ||| | |  || |  | | ||||| |||| |||
ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCCCAAAACTACTCTGTTGAGCTAATCTTGGAACAGgtcaggaccat----gcttcattt-----gag------cctgtttacta------ttgtcttgtgtgattcttatgcatttccgatcttttgtcatccag

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA10G32660.1 (Glycine max), 5'ss of exon 10
ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcgttatcactttttttatcttgagtggttcccccttctttaagcagtttatcttttgtcat-tgtaaccaatgt--ctaccttttctca-ttcag
||||||||||| ||||||||||||||||| || ||||||||  |||  || || |   |||| ||||| || || ||||| ||||| |  ||  ||||     | | ||| ||   | ||       | | |||     ||| | |||   || | |||   |||   || ||  |  ||  |||||
ATGGTTATGGCCGTGTTTGCATACATATATCATCAGTCATTTGTTGTGCCGCAAACTCTCTCGGTTGAAATGATTTTGGACCAGgtaattatatttattttactatgtatattactttgtatatgtatttctaaa----ttaacatttaagatgtttaatttatggaactgccgctgttcgcttcag

upper sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 5'ss of exon 10
ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcgttatcactttttttatcttgagtggttccccctt-ctttaagcagtttatcttttgtcattgtaaccaatgtctaccttttctcattcag-------
||||| ||||| |||||||| ||||| ||||||||||||||  |||  ||||| | ||  || |||||||| || ||| | ||||| |   | |    || | ||  || ||  || ||   ||  |  |   | | |         |||  ||    ||| |  |    ||  || |||  |        
ATGGTGATGGCCGTGTTTGCTTACATCTACCACCAGTCATTTGTTGTTCCTCAAAGCTATTCGGTTGAGATGATTTTGAACCAGgtaaattttg----cattgttgataactataggggccacctgtaaccacagggaacaagaaaattgctatc---acctacatgggtctaatcccataaacaaggggt

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|32806967|gb|CD959201.1|CD959201
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|32809742|gb|CD961976.1|CD961976
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|78079229|gb|DV507641.1|DV507641
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|71760475|gb|DR958412.1|DR958412
EST:     AGTCATTCATTGCACCTCAGAACTTTTCTGTTGAGATAATCTTGGATCAG                         ATTTTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|71426533|gb|DR807583.1|DR807583
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|78121240|gb|DV539624.1|DV539624
EST:     AGTCATTCATTGCACCTCAGAACTTTTCTGTTGAGATAATCTTGGATCAG                         ATTTTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|71426082|gb|DR807132.1|DR807132
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|60338336|gb|DN205309.1|DN205309
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|60344634|gb|DN211607.1|DN211607
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|76014866|gb|DT942036.1|DT942036
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|113702720|gb|EE680224.1|EE680224
EST:     GCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: GCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|76021500|gb|DT948670.1|DT948670
EST:     AGTCATTCATTGCACCTCAGAACTTTTCTGTTGAGATAATCTTGGATCAG                         ATTTTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|76287485|gb|DV027053.1|DV027053
EST:     AGTCATTCATTGCACCTCAGAACTTTTCTGTTGAGATAATCTTGGATCAG                         ATTTTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
EST: gi|7135092|gb|AW497912.1|AW497912
EST:     AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAG                         ATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT
genomic: AGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTT

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: 147

ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTTGGGGAAATGTTCCATGAGAGGCAATTAGGGCAAAACTGAGAGTTAGCGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTTGGGGAAATGTTCCATGAGAGGCAATTAGGGCAAAACTGAGAGTTAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTTGGGGAAATGTTCCATGAGAGGCAATTAGGGCAAAACTGAGAGTTAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

ATGGTTATGGCAGTGTTTGCATACATATACCACCAGTCATTCATTGCACCTCAGAACTTCTCTGTTGAGATAATCTTGGATCAGgtgaggatcg ... tctcattcagATTCTAAGAAACCTGACCTATGAGGAGCAAAAATACCTATATGAACAACTTGGGGAAATGTTCCATGAGAGGCAATTAGGGCAAAACTGAGAGTTAGCGT