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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTTCTGACACACCATTATTGGCCGCGGAAAAGATGAGAGAGGCTCAATCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcacaacattcatataacctccacagtttgtattttagttttcattaatgccactagcctactaagcttgttgaattgtttacaaatgttactc...

Basic information

species Zea mays
transcript GRMZM2G109284_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109284_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g30730.1 (Oryza sativa), 5'ss of exon 10
AATCTTCTGACACACCATTATTGGCCGCGGAAAAGATGAGAGAGGCTCAATCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcacaacattcatataacctccacagtttgtattttagttttcattaatgccactagcctactaagcttgttgaattgtttacaaatgttactc---
 ||||||||||||||||||| || | ||||| |||||||||||||||||| |||  |   |||||||||||||  |||||||||||||||||||| |||||||||  ||||  || | | || | |||| ||||  ||||||| ||||| ||   |   ||    |   ||   | ||||  | ||   |    ||| |    
TATCTTCTGACACACCATTAATGTCTGCGGAGAAGATGAGAGAGGCTCAAGCTCTCAGCAAAACACCATACCTTGTTTTAAGTGGCAATGCAAAATCAGGgtatgtccacagtatacttcta-catcca-agttcttattttaattttccttc-cgatgctgctttttaaattattttgatgtcttccaaggccttaatggaa
















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|24768397|gb|CA403526.1|CA403526
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|32858341|gb|CD998022.1|CD998022
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|32915382|gb|CF020194.1|CF020194
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|67015766|gb|CO444515.1|CO444515
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|40303475|gb|CK347862.1|CK347862
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|32907200|gb|CF012013.1|CF012013
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|32907199|gb|CF012012.1|CF012012
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|14245628|gb|BG874210.1|BG874210
EST:     TCTCGTAATCAAACGCCATACCTCATTTTAAGTGGCAATGCAAAAGCAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|5816421|gb|AI987337.1|AI987337
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
EST: gi|60337809|gb|DN204782.1|DN204782
EST:     TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGG                         TCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG
genomic: TCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGG

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), 47 (downstream exon)
Score: 116

AATCTTCTGACACACCATTATTGGCCGCGGAAAAGATGAGAGAGGCTCAATCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 69

AATCTTCTGACACACCATTATTGGCCGCGGAAAAGATGAGAGAGGCTCAATCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

AATCTTCTGACACACCATTATTGGCCGCGGAAAAGATGAGAGAGGCTCAATCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

AATCTTCTGACACACCATTATTGGCCGCGGAAAAGATGAGAGAGGCTCAATCTCGTAATCAAACACCATACCTCATTTTAAGTGGCAATGCAAAAACAGGgtatgctcac ... tttattttagTCAAACAAGTGATAGCGGCGGCTATGCTACCTTGGAGACAGAGCAACCTGGGAGCCTAACGCCCATGCTTGGGGACAAAAAG