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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgtcattctcatatgtgtaacatattgtgcacctgagttggtactgcctttttatcttacacaaggaatactcttccag

Basic information

species Zea mays
transcript GRMZM2G043056_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043056_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 5'ss of exon 10
CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgtcattctcatatgtgtaacatattgtgcacctgagttggtactgcctttttatcttacacaaggaatactcttccag------
||||||| |  |||||||||||  | ||| ||  ||    |||||||||||| | ||||| |||||||||||||| ||||||| |||||   ||| | ||||||| ||  |||||||||||  |  |  ||||||| | ||||     |  ||   ||||  || ||   |  |||  | | |||       
CTTTACTTCGTTATATCCACCAGGACCTCAAACAATAGGGGGTTGGCAGAGAACACCCCAATTTGGAATGGGATATGCCATGCCATATCAGACTGCAATGgtatctat--cattctcatattagcgatttattgtgtatctga-----tgttgatgtttttcctaactagataaattatttaccaattttag
















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|20811142|gb|BQ295620.1|BQ295620
EST:     GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
EST: gi|60357017|gb|DN223990.1|DN223990
EST:     GAGCCCCCCATTTTGGAATGGGATACGCCGTGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
EST: gi|60338909|gb|DN205882.1|DN205882
EST:     ATGGGATACGCCATGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: ATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
EST: gi|31355485|gb|CD439842.1|CD439842
EST:     GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
EST: gi|22545636|gb|BU097995.1|BU097995
EST:     GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
EST: gi|5566802|gb|AI881668.1|AI881668
EST:     GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
EST: gi|31361667|gb|CD446024.1|CD446024
EST:     GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTG                         TTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT
genomic: GAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATAT

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), 48 (downstream exon)
Score: 307

CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATATTCGCAACATGCATATTCCCACCCCCAACCTGTGAAAGCTTCAAACCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATATTCGCAACATGCATATTCCCACCCCCAACCTGTGAAAGCTTCAAACCCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 113

CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATATTCGCAACATGCATATTCCCACCCCCAACCTGTGAAAGCTTCAAACCCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 143

CTTTACTGCACTATATCCACCATCAACTCCAATGATGCCTGGTTGGCAGAGAGCCCCCCATTTTGGAATGGGATACGCCATGCAATATCCACCTGGAGTGgtatccatgt ... actcttccagTTCCAGGGAATGCAAGCATATCCTCAGCCTACATATCAGCAACCTGTATATTCGCAACATGCATATTCCCACCCCCAACCTGTGAAAGCTTCAAACCCTT