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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaaagaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag

Basic information

species Zea mays
transcript GRMZM2G479243_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 12
GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaa----agaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag
||||| || ||||||||||||||||| |||||||| |||||||||||  |||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||  ||   |||||| | ||| ||  | || ||||    || |   |||   || ||||    | ||| |  |   ||| ||| |    ||   || |||| | | |  ||||||||||||||  |   |||||| |||   | |||
GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaaactgttctgtttcattcattgtgggaaaataacagcatataacaaatgcttaccaccttattgcatctctggattttat----ttatcaatatataatttcatatgctctgagctaattt--gcaaaattcaaaatc-cag

upper sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA01G35390.1 (Glycine max), 5'ss of exon 11
GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaaagaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag
|| || || || || || ||||||||||| || ||| | ||||| |||||||| || ||||| || || ||||| ||||| ||||||||||| || ||||||| |   | || |      ||     |   |  | | |   | |  ||    |  |  | | |  |       | | | ||   ||  ||  | || | ||   | |                                       
GATGCTCGGGTCTCTGATTTTGGACTTGCCAAACTTCTGGAGGATGAAGAATCTCACATCACCACTATTGTTGCTGGAACGTTTGGTTATCTAGCTCCAGgtaggca-atgtagaatgaatatgat-atttgccagatagatagttgaccggggcatgatttgtggt----atttagcatttaaacta-ttaatgaagt-tcttcgtt---------------------------------------

upper sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA09G34940.2 (Glycine max), 5'ss of exon 12
GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaaagaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag
||||| || || || || ||||||||||| || ||| | ||||| |||||||| || ||||| || || ||||| ||||||||||||||||| || ||||||| |   |   |  |       ||  |   |  | | |   | |   |    |  |  | | |  |       | | | ||   ||  ||  | || | ||  || |                                       
GAGGCTCGGGTCTCTGATTTTGGACTTGCCAAACTTCTGGAGGATGAAGAATCTCACATCACCACTATTGTTGCTGGAACATTTGGTTATCTAGCTCCAGgtaagcaaagcacaatgaatatgat--atttgtcagatagatagttggccggggcatgatttgtggt----atttagcatttaaacta-ttaatgaagt-tctttgtt---------------------------------------

upper sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT2G35620.2 (Arabidopsis thaliana), 5'ss of exon 12
GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaaagaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag
||||| || |||||||||||||| ||||| ||| | ||||||||||||||||| ||||| || || || |||||||| ||||| |||||  | || |||||||      | |    | |  | | | |        |   |   | |   ||||||    | | |||  |||    | |||     ||  || |    | |  | |                                         
GAGGCTCGGGTATCAGACTTTGGGCTTGCCAAGTTGTTAGAGGACGAAGAATCTCATATTACAACCATTGTTGCAGGCACATTCGGTTACTTGGCTCCAGgtactc---aattacacagtaataacaatgcttattacttgttgttactatctgttaggacctaaat--ccgt---gaactcataatgagtgtt----ttttgcag-----------------------------------------

upper sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT1G31420.2 (Arabidopsis thaliana), 5'ss of exon 12
GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaagtcgttctgctacatccagaggggaaaaaagaaatgaacttctgtttactctttaattaccgcatcggactttctctggttgctaaaatatcactgctaatgctctgagctaacatcaacaaaatccaactccacag
||||| || ||||| || ||||| || || ||| | || || ||||||||||| |||||||| || || |||||||| |||||||| || || || |||||||  |  | | | ||     |  ||   |     | |||||  ||| |||     | ||     | |    |||  |||                                                                   
GAGGCACGGGTATCGGATTTTGGTCTAGCCAAGTTGTTGGAAGACGAAGAATCTCATATCACAACCATTGTTGCAGGCACATTTGGGTACCTAGCTCCAGgtacat--atgccttttaa--aagtctttacttacataaagatttgatctttcaaatgctg--agacttttccatttgacag-----------------------------------------------------------------

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|14203819|gb|BG837496.1|BG837496
EST:     ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
EST: gi|4753348|gb|AI657253.1|AI657253
EST:     ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCG
EST: gi|149112041|gb|EE191208.2|EE191208
EST:     ATCCCATATCACTCCAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
EST: gi|13382220|gb|BG458895.1|BG458895
EST:     ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
EST: gi|60351981|gb|DN218954.1|DN218954
EST:     ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
EST: gi|116827567|gb|EC871481.1|EC871481
EST:     ATCACATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
EST: gi|60395535|gb|DN228405.1|DN228405
EST:     ATCACATATCACCACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
EST: gi|101389569|gb|EB816717.1|EB816717
EST:     ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAG                         AGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG
genomic: ATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTG

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: 48 (upstream exon), 47 (downstream exon)
Score: 118

GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 43

GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

GAGGCCCGCGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGACGAAGAATCCCATATCACTACAATAGTTGCAGGAACATTTGGTTATCTTGCGCCAGgtatgtggaa ... aactccacagAGTATATGCAGTTTGGCAGAGCCACCGAGAAGACCGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATC