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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTCGGACACCAATCATTGTATTTACGCAGACAGGCTCCATGGCTGTCCTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcctttgtggttccccttcacgacaataacaccatctttaacgcgatattgagatcatcagttcatagccttcatgaatcagatgatctaaataggcaaatatggtctgaagtacacttgacatttaggggaactgaactatcgttgttgcag

Basic information

species Zea mays
transcript GRMZM2G144730_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 10
CCCTTCGGACACCAATCATTGTATTTACGCAGACAGGCTCCATGGCTGTCCTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcctttgtggttccccttcacg-acaataaca------ccatctttaacgcgata--ttgagatcatcagttc-atagccttcatgaat---cagatgatctaaataggcaaatatggtctgaagtacacttgacatttaggggaactgaactatcgttgttgcag
||||| | || ||||| ||||| ||||| |  || ||||||||||| ||||| || |||||||| || |||||||||||||| ||||| |||||||| |||| ||||  |||  | || |     ||   ||||  ||         ||  ||  |   |   || ||   |||| ||   ||  | |  | |||    | |||||  || | |  ||| ||| |||| || ||   ||||  ||| | | |   |||| | ||||  |   
CCCTTTGCACCCCAATTATTGTGTTTACACGAACCGGCTCCATGGCAGTCCTTCTCAGCCACTACCGGCCCTCGTCTACAATTTTTGCATTTACAAATGAgtaagttttttttggatttctacctacatgcaatgccaaatcttttttccctagtgttttcattttagtaaatcaattttgtaaacattctaaataaataaatgataaaagttgaaaaagatgctctggaggac---tgaccattatgagga---aactgttgttgcag---
















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|60338877|gb|DN205850.1|DN205850
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|71764040|gb|DR961977.1|DR961977
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|7227784|gb|AW566425.1|AW566425
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCAACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|7238117|gb|AW573339.1|AW573339
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCAACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|32860149|gb|CD999830.1|CD999830
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|32860148|gb|CD999829.1|CD999829
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|60400196|gb|DN233003.1|DN233003
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|148966756|gb|EE017836.2|EE017836
EST:     CTCCTGAGCCACTATCGTCCCTCGTTTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTTTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|148958743|gb|EC905020.2|EC905020
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|32934959|gb|CF039771.1|CF039771
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|32931620|gb|CF036432.1|CF036432
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
EST: gi|60344484|gb|DN211457.1|DN211457
EST:     CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGA                         GGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA
genomic: CTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCA

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: 185

CCCTTCGGACACCAATCATTGTATTTACGCAGACAGGCTCCATGGCTGTCCTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 139

CCCTTCGGACACCAATCATTGTATTTACGCAGACAGGCTCCATGGCTGTCCTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 107

CCCTTCGGACACCAATCATTGTATTTACGCAGACAGGCTCCATGGCTGTCCTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

CCCTTCGGACACCAATCATTGTATTTACGCAGACAGGCTCCATGGCTGTCCTCCTGAGCCACTATCGTCCCTCGTCTACAATATTTGCGTTTACAAACGAgtgagttcct ... gttgttgcagGGAACGAGTGAAGCTACGGCTAGCACTCTACCAGGGGGTCATCCCTATTCACATGGAGTTCTCTGACGACGCAGAAGAAACTTTCTCCAGAGCAATTAGC