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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCTCGCGCCCGCTCGAGGACGCCGTCGTGGATTTCCTCGCACGCGTGCCCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtctctttgtgatcagagaccctctccgccgcttttgtctagttttatgcgtcgctcttgttgtagccgcgtgtcgttggattgttgggttatc...

Basic information

species Zea mays
transcript GRMZM2G133757_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133757_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 5'ss of exon 1
CGTCTCGCGCCCGCTCGAGGACGCCGTCGTGGATTTCCTCGCACGCGTGCCCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtg-cgtgtctctttgtgatcagagaccctctccgccgcttttgtctagttttatgcgtcgctcttgttgtagccgcgtgtcgttggattgttgggttatc--
|||   ||||||||||||||||| ||| | ||| |||||||| ||| | |  || ||||||||| |||| || ||| ||||||| | |||||||||| ||||  |  | | ||   ||    | ||  | | ||  ||||   | |        | ||||   |||| ||   ||  ||       ||  |   | |   |  
CGTGAAGCGCCCGCTCGAGGACGTCGTGGCGGACTTCCTCGCCCGCATCCAGCCCGAGCGCCGCCTCCGCTTCGGCGCCGCCATAAACTTCGTCCTCAAGgtaacccgcccctccctggattg-gattccccccctcgctcccgcccgcccgcgt-cgtc-tgcttgatgcctcctggttcgaggcgagcgcccgctcggctt
















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|211505373|gb|FL332381.1|FL332381
EST:     CCCCAGAGCGCCGCTTCC--TTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|74240369|gb|DT648283.1|DT648283
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|74237046|gb|DT644960.1|DT644960
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|91051391|gb|EB161809.1|EB161809
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|37423952|gb|CF649706.1|CF649706
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|76289049|gb|DV028617.1|DV028617
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|78110369|gb|DV528781.1|DV528781
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|76285618|gb|DV025186.1|DV025186
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
EST: gi|101395524|gb|EB819690.1|EB819690
EST:     CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAG                         GACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG
genomic: CCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTG

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), 45 (downstream exon)
Score: 59

CGTCTCGCGCCCGCTCGAGGACGCCGTCGTGGATTTCCTCGCACGCGTGCCCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTGCATCAAGGTTATTCCTCACAGTCGGCAAATCCATTTCTTCCTCTCTTAA


Block sizes: 40 (upstream exon), 46 (downstream exon)
Score: 13

CGTCTCGCGCCCGCTCGAGGACGCCGTCGTGGATTTCCTCGCACGCGTGCCCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTGCATCAAGGTTATTCCTCACAGTCGGCAAATCCATTTCTTCCTCTCTTAA


Block sizes: 47 (upstream exon), 27 (downstream exon)
Score: 13

CGTCTCGCGCCCGCTCGAGGACGCCGTCGTGGATTTCCTCGCACGCGTGCCCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTGCATCAAGGTTATTCCTCACAGTCGGCAAATCCATTTCTTCCTCTCTTAA


Block sizes: 42 (upstream exon), 47 (downstream exon)
Score: 19

CGTCTCGCGCCCGCTCGAGGACGCCGTCGTGGATTTCCTCGCACGCGTGCCCCCAGAGCGCCGCTTCCGGTTTGGCTCCGCCATTAGCTTCGTCCTCGAGgtgcgtgtct ... ctctaatcagGACAAAATGATGCTTCAACCTGCTGAGCGTTTAGTTGCATTTGCAATTCTGCATCAAGGTTATTCCTCACAGTCGGCAAATCCATTTCTTCCTCTCTTAA