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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaacccccctcctttcatttggtcaatcaatccgtcaaattagttcatatccttagtttgatgttattatgaaggaattgtttcttggtcggtgcag

Basic information

species Zea mays
transcript GRMZM2G040613_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040613_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g34840.1 (Oryza sativa), 5'ss of exon 1
CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgt--gctaggaa---------cccccctcctttcatttggtc----------aatcaatccgtcaaattagttcatatccttagtttgatgttattatgaaggaat--tgtttcttggtcggtgcag--------------------
|||||||||||||||||||||||| ||||| |||||||||| | | ||||||||||| |||||| |||||||| | ||||| ||||||||||||||||||||  | | ||           |||||| ||  ||   || ||           || | ||| || |||| || |   | ||| |||||||  | || ||| |  ||  || |||||||  |||                        
CTGCGCGTACGGCTCCACGCTCCTCCACGCCCGCCCCGACGCGTCCTCCATGGTCGACTACATCCTCGGCGTCCCCGACCCGCTCCAGTGGCACTCCGAGgtagggtgggtgactgagcccccccccccccctctcctgttctactcttccagattattccatccaattggtcccc-ttcttggtttgatactctt-tgatgcgatcttggttcttggatggtttcttggttggttaattggtgcag

upper sequence: GRMZM2G040613_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g34760.1 (Oryza sativa), 5'ss of exon 1
CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtg----------ctaggaacccccctcctttcatttggtc----------aatcaatccgtcaaattagttcatatccttagtttgatgttattatgaaggaat--tgtttcttggtcggtgcag--------------------
|||||||||||||||||||||||| ||||| |||||||| | | | ||||||||||| |||||| |||||||| | ||||| ||||||||||||||||||||           ||  |  |||||| ||  |    || |            || | | | || |||| || |   | ||| |||||||  | || ||| |  ||  || |||||||  |||                        
CTGCGCGTACGGCTCCACGCTCCTCCACGCCCGCCCCGAAGCGTCCTCCATGGTCGACTACATCCTCGGCGTCCCCGACCCGCTCCAGTGGCACTCCGAGgtagggtgggtgactgagccccccccccccctttcctgttttactcttccagattatttcctccaattggtcccc-ttcttggtttgatactctt-tgatgcgatcttggttcttggatggtttcttggttggttaattggtgcag

upper sequence: GRMZM2G040613_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g22960.1 (Oryza sativa), 5'ss of exon 1
CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa----------cccccctcctttcatttggtca---------atcaatccgtcaaattagttcatatccttagtttgatgttattatgaaggaatt----gtttcttggtcggtgcag
||||||||||||||| || ||||| ||||| ||| ||| || | | |||||| |||| |||||| ||||| || | ||||| ||||||||||||||||||||     ||           |||||| ||   || ||    |         || ||||| || |||| |  |   || ||  |||||||  ||  || | |  ||    |||  ||| | |||||||
CTGCGCGTACGGCTCAACCCTCCTCCACGCGCGCTCCGGCGCGGCCTCCATGATCGACTACATCCTCGGCATCCCCGACCCGCTCCAGTGGCACTCCGAGgtagggtgattgatcacccccccccccccccccacttttctactcttccagattaatccatccaattggcccccttctttgatttgatgcgatcttggacggtttcttggttgattgattggtgcag

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|76914432|gb|DV165525.1|DV165525
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|71325073|gb|DR799221.1|DR799221
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|148932495|gb|EC876262.2|EC876262
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|76293091|gb|DV032659.1|DV032659
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|211395667|gb|FL294626.1|FL294626
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|89759612|gb|DY688380.1|DY688380
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|211393052|gb|FL294622.1|FL294622
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|78112418|gb|DV530812.1|DV530812
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|211395666|gb|FL294625.1|FL294625
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|211393053|gb|FL294623.1|FL294623
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAG                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTCCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
EST: gi|88749010|gb|DY533151.1|DY533151
EST:     TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAA                         AACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT
genomic: TGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGT

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: 45 (upstream exon), 48 (downstream exon)
Score: 16

CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGTGCAGGCGCC


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 8

CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGTGCAGGCGCC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 12

CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGTGCAGGCGCC


Block sizes: 45 (upstream exon), 41 (downstream exon)
Score: 17

CTGCGCGTACGGCTCCACGCTCCTTCACGCACGCCCCGACGGGACGTCCATGGTCGATTACATCATCGGCGTCGCTGACCCCCTCCAGTGGCACTCCGAGgtgctaggaa ... gtcggtgcagAACCTGGAAAGGAACCCCGCGCACTACTCCCGCTGGATGGCCGGCTTCGGTGCAGGCGCC