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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgtcgatatgatccgtcgtctttgctggctgtacatgctaactttccatcgcttcttggatgcaatgcaacag

Basic information

species Zea mays
transcript GRMZM2G067022_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067022_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g37470.1 (Oryza sativa), 5'ss of exon 6
CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgtcgatatgatccgtcgtctttgctggctgtacatgctaactttcca---tcgcttcttggatg-caatgcaacag------------------
|||||||||||||||||||||||||||||||||||||||||||||| ||||||| ||||| ||||||| ||||||||||||||||| ||||||||||||||||| |||| | | || | | |||| || ||| || | || | || || |||| | |
CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACATCATCCCCTCCCTCTCCCACATCCTCACGTACCGCTCCGCCTCCGCCAGATTGgtaagtgtgtgcagcta--cctttgccttttctttacttaccattaaattgcccgagtagattcctcatatatcaatatgaaacatgcactgtttgtctaaa

upper sequence: GRMZM2G067022_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G01240.2 (Arabidopsis thaliana), 5'ss of exon 6
CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgtcgatatgatccgtcgtctttgctggctgta---catgctaact-ttccatcgcttct-tggatgcaatgcaacag-----------------
|| ||||| || || || || | || || | |||||||||||| ||||||| ||| | ||||||||||||||||||||| |||| || ||| | |||| | | | || | || | || || |||| || || ||| | |||| || ||
AATAAACTCGGCAGTTGGAGCCTTACTTGTTACCTTCACCGTCTATATCATCCCTGCCTTAGCCCACATGCTCACGTACCGCACCGCCTCTGCCCGCCGGgtacctacattcttct--ctcgctcacattaccattcctaaactatactaaagattttatgaattcagtagatgacatacatttatttcatttagatagata

upper sequence: GRMZM2G067022_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ21839 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgtcgatatgatccgtcgtctttgctggctgtacatgctaactttccatcgcttcttggatgcaatgcaacag--------------------------
||||||||||| ||||| ||||||||||||| |||||| ||||| ||||||| | ||||| |||||| ||||||| | | || | |||||| |||||| | ||| | ||| |||| ||| |||| || | | | ||| | | | | ||| ||| | ||
AATCAACTCCGCGGTCGGGGCGCTCCTCGTCACCTTCACTGTCTATATCATCCCCTCGCTCGCACACATGATCACGTATAGAACAGCCTTCGCCAGGGCGgtaagtttctcg-caaaatc--tcgttttt-ctggaagttcttcc--actcctcgtttccttttgagtgccggagatgagattatttttcttgcttgtttctctag

upper sequence: GRMZM2G067022_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ34222 (Selaginella moellendorffii), 5'ss of exon 7
CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgtcgatatgatccgtcgtctttgctggctgtacatgctaactttccatcgcttcttggatgcaatgcaacag---------------------------
||||||||||| ||||| ||||||||||||| |||||| ||||| ||||||| | ||||| |||||| ||||||| | | || | |||||| |||||| | ||| | ||| |||| ||| |||| || | | | ||| | | | | ||| ||| | | ||
AATCAACTCCGCGGTCGGGGCGCTCCTCGTCACCTTCACTGTCTATATCATCCCCTCGCTCGCACACATGATCACGTATAGAACAGCCTTCGCCAGGGCGgtaagtttctcg-caaaatc--tcgttttt-ctggaagttcttcc--actgctcgtttcct-ttgagtgccaaagatgagattttttttcttgcttgtttctctgag

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|78113175|gb|DV531569.1|DV531569
EST:     TCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTG                         AACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTC
genomic: TCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTC
EST: gi|91870568|gb|EB400952.1|EB400952
EST:     CCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTG                         AAGGCAGCGGAGAAGCCGCCGTCCTTCTTCCCGAGCTGGTCGGGGATGTTC
genomic: CCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTC
EST: gi|149086899|gb|EE176442.2|EE176442
EST:     TCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTG                         AACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTC
genomic: TCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTC

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: 40 (upstream exon), 41 (downstream exon)
Score: 15

CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTCGTGCTGAACGCGTTCGTGGTGGCGTGGATGCTGGTGGTTGGATTCGGCC


Block sizes: 49 (upstream exon), 8 (downstream exon)
Score: 2

CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTCGTGCTGAACGCGTTCGTGGTGGCGTGGATGCTGGTGGTTGGATTCGGCC


Block sizes: 47 (upstream exon), 12 (downstream exon)
Score: 3

CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTCGTGCTGAACGCGTTCGTGGTGGCGTGGATGCTGGTGGTTGGATTCGGCC


Block sizes: 40 (upstream exon), 26 (downstream exon)
Score: 3

CATCAACTCCGCCGTCGGCGCGCTCCTCGTCAGCTTCACCGTCTACGTCATCCCGGCCCTCGCCCACATGCTCACGTACCGCTCCGCGTCCGCCAGATTGgtaagcgtgt ... aatgcaacagAACGCAGCGGAGAAGCCGCCGTCCTTCTTGCCGAGCTGGTCGGGGATGTTCGTGCTGAACGCGTTCGTGGTGGCGTGGATGCTGGTGGTTGGATTCGGCC