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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGATTGGGGAGATTGCCAATTTTGTGGCCTACATGTTTGCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgtgaatatgtgattgctaaatgacttaatctgttatatatcatgtggtcatgtggagagtggatatggttaaatattttgtgtattttctttccttttctttaaaaaaacatgtacatgctcctgtatatgatctctatggtctatggagcag

Basic information

species Zea mays
transcript GRMZM2G097421_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097421_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g35570.1 (Oryza sativa), 5'ss of exon 3
TGCTGATTGGGGAGATTGCCAATTTTGTGGCCTACATGTTTGCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgtgaatatgtgattgctaaatgacttaatctgttatatatcatgtggtcatgtggagagtggatatggttaaatattttgtgtattttctttccttttctttaaaaaaacatgtacatgctcctgtatatgatctctatggtctatggagcag
|||| ||||| |||||||| ||||| ||||| |||||||| || || ||| |||| || || || || || || |||||||||||||| |||||  | || | || |||          |  |||    ||| | || || ||  || |      ||    ||    | || || |||   | | | | | |   | | |    ||  | |   | |  |   | |                          
TGCTCATTGGTGAGATTGCAAATTTCGTGGCTTACATGTTCGCACCGGCTGTTCTGGTTACTCCCCTCGGCGCTCTCAGCATAATTGTTAGgtacaactg-ggatgtgt----------tccctttgcttgtaaaatttcctg--gtta------gaacccatggtttgaattagttttaatctgtccatgcacatgcgtggtgaatgcgtaatctttgtggagcag-------------------------
















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|78118379|gb|DV536765.1|DV536765
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|101399470|gb|EB821607.1|EB821607
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|149012854|gb|EE042696.2|EE042696
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|211193189|gb|FK988934.1|FK988934
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGARAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|71305814|gb|DR789035.1|DR789035
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|211193198|gb|FK988943.1|FK988943
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCAWTTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTG
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCA-TTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTG
EST: gi|91048854|gb|EB159272.1|EB159272
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|211193195|gb|FK988940.1|FK988940
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|74236901|gb|DT644815.1|DT644815
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|149101364|gb|EE187481.2|EE187481
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|148951157|gb|EC896836.2|EC896836
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|40334623|gb|CK368693.1|CK368693
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTTT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|148947645|gb|EC893125.2|EC893125
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|74244190|gb|DT652104.1|DT652104
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|148942011|gb|EC887002.2|EC887002
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|71416856|gb|DR803834.1|DR803834
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|148972078|gb|EE022933.2|EE022933
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|149005298|gb|EE039847.2|EE039847
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|149070089|gb|EE158489.2|EE158489
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|91050129|gb|EB160547.1|EB160547
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|211193191|gb|FK988936.1|FK988936
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|149013793|gb|EE043260.2|EE043260
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|148948891|gb|EC894305.2|EC894305
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|211193199|gb|FK988944.1|FK988944
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|94477226|gb|EB706184.1|EB706184
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|211190794|gb|FK988929.1|FK988929
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGKTCTAGCCCATTTCACCCTGAATGARAAGCTGCARCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|101394371|gb|EB819120.1|EB819120
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTG
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCC-ATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTG
EST: gi|33285537|gb|CF075332.1|CF075332
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGCCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|71446398|gb|DR827448.1|DR827448
EST:     CGCCAGCCTATTCTTGTCACCCCTCTTGGTGCGCTCAACATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATG
genomic: CGCCAGC-TATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATG
EST: gi|78079716|gb|DV508128.1|DV508128
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|71446399|gb|DR827449.1|DR827449
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|76012865|gb|DT940035.1|DT940035
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
EST: gi|50323304|gb|CO518430.1|CO518430
EST:     GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAG                         TGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT
genomic: GCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGT

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: 88

TGCTGATTGGGGAGATTGCCAATTTTGTGGCCTACATGTTTGCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGTGTTGGGCTGTGTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

TGCTGATTGGGGAGATTGCCAATTTTGTGGCCTACATGTTTGCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGTGTTGGGCTGTGTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

TGCTGATTGGGGAGATTGCCAATTTTGTGGCCTACATGTTTGCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGTGTTGGGCTGTGTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

TGCTGATTGGGGAGATTGCCAATTTTGTGGCCTACATGTTTGCGCCAGCTATTCTTGTCACCCCTCTTGGTGCGCTCAGCATAATTGTCAGgtaggattgt ... tatggagcagTGCTGTTCTAGCCCATTTCACCCTGAATGAGAAGCTGCAGCGGATGGGTGTGTTGGGCTGTGTGCTCTGTATAATCGGGTCAACCATAATCATCCTCCAT