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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccttaccatgtcaatcacatggactggtgtgggtatagcttgttcctcaacgaacactatattattagctgtgattatacatataatattgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG

Basic information

species Zea mays
transcript GRMZM2G017853_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017853_T01 (Zea mays), 3'ss of exon 6
lower sequence: 13113.m00225 (Oryza sativa), 3'ss of exon 6
---------gtccttaccatgtcaatcacatggactggtgtgggtatagcttgttcctcaacgaacactatattattagctgtgattatacatataatattgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG
         | | ||  |||||  ||  |||||      |||| |||   | | |  | ||  | |  | || |||| | ||| ||| |   |   | ||| ||  ||||||||||| ||||||||  | || || |||||||||||||   || ||||||| ||| |||| |||||||| ||||| ||||||||
ttccccatgggctttttcatgttcattgcatggg-----gtggctatga-tggctgtttaattagctgt-tagtattgg-tgtaattctttgtggta-attatttgcagGATGCTGCTTCCCTTGCAATTGCCATAATGAAAAAGGGACACAGGGGTCGAATCTTTTTGGGCTGTGACAATAAGCCTCTTTCCAG
















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|74233405|gb|DT641319.1|DT641319
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|211291636|gb|FL460652.1|FL460652
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|71437097|gb|DR818147.1|DR818147
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGAATCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCAT
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCAT
EST: gi|18177348|gb|BM378558.1|BM378558
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|76927174|gb|DV171165.1|DV171165
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|71310881|gb|DR791743.1|DR791743
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|78089273|gb|DV517647.1|DV517647
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|78082079|gb|DV510491.1|DV510491
EST:     GGACTTTAGACACACGACCAGATCATATCATCAACCAGAATCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAG
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAG
EST: gi|71310883|gb|DR791744.1|DR791744
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCTCTTGCT
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCT
EST: gi|74233404|gb|DT641318.1|DT641318
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|211289510|gb|FL460651.1|FL460651
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|101382998|gb|EB813552.1|EB813552
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCT
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCT
EST: gi|76927172|gb|DV171164.1|DV171164
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTGGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|91051135|gb|EB161553.1|EB161553
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCGGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGGGGAGTGGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|71764490|gb|DR962427.1|DR962427
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA
EST: gi|78085441|gb|DV513834.1|DV513834
EST:     GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAG                         GATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGAATGGGGAGTGGA
genomic: GAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 107

AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 81

AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 73

AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 58

AAGATAGACAGAGGTGCACATGTTTTCTGGTTGAGGAAAGGAACTTTAGACACACGACCAGATCATATCATCAACCAGATTCATTATGAGgtacagattt ... ttgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcaacgaacactatattattagctgtgattatacatataatattgttgccagGATGCTGCCTCCCTTGCTGTAGCAATCATGAAAAAGGGACTGCGGAGTCGAATATTTCTGGGTTGTGACAACAAGCCCCTTTCCAG
                            tgattatacatataat  TA-rich tract