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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctgcttcgcgtgcgccttcttcgttgcgcgggttgtgggctcgggtggtggctactagagtgagagaggaccaggagcgaggagagcgtgctc...

Basic information

species Zea mays
transcript GRMZM2G083095_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083095_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 1
GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctgcttcgcgtgcgccttcttcgttgcgcgggttgtgggctcgggtggtggctactagagtgagagaggaccaggagcgaggagagcgtgctc---
|| ||| ||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||||||| || |||| | | ||||| || | | | | | || | || || | || | |||| | ||| | || | |
GGGCACAAGCACCTCTCCGGCCTCGATGAGGCCGTCCTCAAGAACATCGACGCCTGCCGCGAGCTCTCCGCCATCACCCGCACCTCCCTCGGCCCCAACGgtgaggcccccttccct--ctccttccccgctctgtgctccggcgtcttcgttgcccgcgttttga-tccgagaagtttgggatctagcgatgtgccacggcg
















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|211339979|gb|FL217829.1|FL217829
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|211342372|gb|FL217845.1|FL217845
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|211342371|gb|FL217844.1|FL217844
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|211342368|gb|FL217841.1|FL217841
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|211339980|gb|FL217830.1|FL217830
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|211339977|gb|FL217827.1|FL217827
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|211339982|gb|FL217832.1|FL217832
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
EST: gi|148978584|gb|EE026233.2|EE026233
EST:     CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACG                         GAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG
genomic: CGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACG

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: 48 (upstream exon), 49 (downstream exon)
Score: 218

GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 86

GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

GGCCACCGCCACCTCTCCGGGCTCGAGGAGGCCGTTCTCAAGAACATCGACGCCTGCCGCGAGCTGTCCGCCATTACGCGCACCTCTCTCGGCCCGAACGgtgagtcctg ... ctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA