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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaagtccctctgttacatcctgaggggaaagagaagaaatgaacttctgtttactctttaatcgccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacag

Basic information

species Zea mays
transcript GRMZM5G886952_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 12
GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaagtccctctgttacatcc--tgaggggaaagagaagaaatgaacttctgtttactctttaatcgccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacag
||||| |||||||||||||||||||| |||||||| |||||||| ||  |||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||  ||     |||||| ||| |  || ||| ||| |  || |   |||   || ||||    | || ||  ||   || ||| |    ||   || |||| |||    ||||||||||||||      | |||| | ||  | |||
GAGGCTCGTGTATCAGACTTTGGACTCGCAAAGCTATTAGAGGACGACAAATCCCATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAGgtatgttaaaactgttctgtttcattcattgtgggaaaataacagcatataacaaatgcttaccaccttattgcatctctggattttat----ttatcaatatataatttcatatgctctgagctaattt--gcaaaattcaaaatc-cag

upper sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA09G34940.2 (Glycine max), 5'ss of exon 12
GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaagtccctctgttacatcctgaggggaaagagaagaaatgaacttctgtttactctttaatcgccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacag
||||| || || || || ||||||||||| || ||| | |||||||||||||| || || || || || ||||| ||||||||||| || || || ||||||| |   |   |  |   |   ||  |     || |||     | |   |    |  |  | | |  |      || ||  |||      ||  | || | || |||||                                       
GAGGCTCGGGTCTCTGATTTTGGACTTGCCAAACTTCTGGAGGATGAAGAATCTCACATCACCACTATTGTTGCTGGAACATTTGGTTATCTAGCTCCAGgtaagcaaagcacaatgaatatgatatttgtcagataga----tagttggccggggcatgatttgtggta-----tttagcatttaaactattaatgaagt-tctttgtt---------------------------------------

upper sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT2G35620.2 (Arabidopsis thaliana), 5'ss of exon 12
GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaagtccctctgttacatcctgaggggaaagagaagaaatgaacttctgtttactctttaatc-gccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacag
||||| || |||||||||||||| ||||| ||| | |||||||| |||||||| |||||||| || || |||||||| ||||| || ||| | || |||||||      | |  | | || | | |   | |   |  |   |   | |   ||||||    | | |||| |     ||| | |   | |  ||   |                                                    
GAGGCTCGGGTATCAGACTTTGGGCTTGCCAAGTTGTTAGAGGACGAAGAATCTCATATTACAACCATTGTTGCAGGCACATTCGGTTACTTGGCTCCAGgtactc---aattacacagtaataac--aatgcttattacttgttgttactatctgttaggacctaaatccgtgaactcataatgagtgttttttgcag---------------------------------------------------

upper sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv02s0087g00170.t01 (Vitis vinifera), 5'ss of exon 12
GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa-gtccctctgttacatcctgaggggaaagagaagaaatgaacttctgtttactctttaatcgccgcttcagactttctctggttgctaaaatatcattgttaatgctctgagctaacaccaacgaaatccgaatccacag
||||| || ||||| |||||||||||||| ||  | || |||||||| ||||| |||||||| || || || |||||||| ||||| ||  | || ||||||  ||           ||||| ||||         |     |  ||||   |||   ||     ||       | |  ||||||  |  |  || || || || ||                                           
GAGGCTCGAGTATCTGACTTTGGACTTGCTAAATTGTTGGAGGATGAGGAATCTCATATTACAACCATTGTAGCAGGAACTTTTGGTTATTTGGCTCCAGgtgagtaatgtagtaaactgtt-catctcacatattatatttaagaatg---ttccaattggcacttggcttttgat--agacttgatg-gaatggtagaaaatgat-------------------------------------------

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|31357285|gb|CD441642.1|CD441642
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|32934260|gb|CF039072.1|CF039072
EST:     ATCACATACTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|211113783|gb|FL295736.1|FL295736
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|211113784|gb|FL295737.1|FL295737
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAG-CACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|24767488|gb|CA402630.1|CA402630
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTCCCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|24763969|gb|CA399139.1|CA399139
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|60342589|gb|DN209562.1|DN209562
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTATCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|37395990|gb|CF635282.1|CF635282
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|60396674|gb|DN229542.1|DN229542
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|61119688|gb|DN560649.1|DN560649
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|60348288|gb|DN215261.1|DN215261
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG
EST: gi|149109165|gb|EE293168.2|EE293168
EST:     ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAG                         AGTATATGCAATTTGGCAGAGCCCCCGAGAAGACTGATGTCTACAGTTTTG
genomic: ATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTG

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), 49 (downstream exon)
Score: 153

GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTGGGGTTTTGGTACTCGAAATACTCAGTGGAAAGCGGCCTACTGATGCATC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTGGGGTTTTGGTACTCGAAATACTCAGTGGAAAGCGGCCTACTGATGCATC


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 41

GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTGGGGTTTTGGTACTCGAAATACTCAGTGGAAAGCGGCCTACTGATGCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GAGGCCCGTGTATCAGACTTTGGACTTGCAAAGCTTTTAGAGGATGAAGAATCACATATTACTACAATAGTTGCAGGAACATTTGGCTACCTTGCACCAGgtatgtggaa ... gaatccacagAGTATATGCAATTTGGCAGAGCCACCGAGAAGACTGATGTCTACAGTTTTGGGGTTTTGGTACTCGAAATACTCAGTGGAAAGCGGCCTACTGATGCATC