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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttatgtctgattattttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacatcaggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag

Basic information

species Zea mays
transcript GRMZM2G573867_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 5'ss of exon 5
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttatgtctgatt--attttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacat-caggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
||| |||||||| ||||||||||||||||| ||||| || || || |||||||||||||| || ||||||||||| || || || || ||||||||||||||| || |||||||       |   ||||  |||||  ||  |  |||    |  ||||   |        | ||      |||  ||||  ||    | |||||    |  |                                                               
TATTAAGAGATCGTGTGAAAACAAAGCTGAAGTGGTTGCTCAGGACGAGAAGGAAAGTGGTCTCCGAGCAACACTTAATCTCGGCCATACATTTGGCCATgtaagtattatcat-------taactatggttgattttatgctgaactaatgtcaataaacatt-------ataatgcactccatgtttagtactcgtatgatttgctgggctg--------------------------------------------------------------

upper sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G08350.1 (Glycine max), 5'ss of exon 5
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttatgtctgattattttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacatcaggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
||| ||| |||||||||||||||| |||||||| ||  |   |||||||||||||||||| ||  | |||||| | ||| ||||||| |||||||| |||||  ||| |            | | |||| || ||||||      ||   ||| |||   |  | |    | |   | |  |  ||     ||| ||| ||| | | | |  ||  ||  ||                                                   
TATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtgat------------tgtctatgactaattatt-----atgaggttg-taaaactgtgaaatctgcattctgaaaattttc----cat-aggtttttttacactcctgataatattt--------------------------------------------------

upper sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G08350.2 (Glycine max), 5'ss of exon 5
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttatgtctgattattttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacatcaggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
    ||| |||||||||||||||| |||||||| ||  |   |||||||||||||||||| ||  | |||||| | ||| ||||||| |||||||| |||||  ||| |            | | |||| || ||||||      ||   ||| |||   |  | |    | |   | |  |  ||     ||| ||| ||| | | | |  ||  ||  || | | |                                             
----AAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATGTGAgtgat------------tgtctatgactaattatt-----atgaggttg-taaaactgtgaaatctgcattctgaaaattttc----cat-aggtttttttacactcctgataatatt-tataa---------------------------------------------

upper sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 5
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttat-gtctgattattttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacatcaggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
||| ||| |||||||||||||||| |||||||| ||  |   |||||||||||||||||| ||  | |||||| | ||| ||||||| |||||||| |||||  |||  ||  | | ||  |  ||||  |||||   | |   | |||    |||||  ||    | | ||    | ||  |   |      || |  | ||||                                                                     
TATAAAGCGATCTTGTGAAAACAAGGCTGAGGTTGTGTCCTTAGATGAGAAGGAAAGTGGACTGAGGGCAACATTGAACTTGGGTCATACATTTGGTCATgtgagtg--attgtatatgactggttattatctgaggttgtaaaattgt----gataatatttataacctaggttatgaattattatgtgttgataaacaattata--------------------------------------------------------------------

upper sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 5
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgttatcatgtttggatttttatgtctgattattttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacatcaggatttatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
||| ||| |||| ||||||||||| || || || ||  ||||||||||||| ||||| ||| | ||||||||  ||||  ||||||| || |||||||||||| ||  |  |||| |  | | | |     ||   |||| ||                ||||||   |    |  | | ||||   ||||| |    ||||  |||                                                                  
TATAAAGCGATCATGTGAAAACAAGGCAGACGTTGTATCACAAGATGAGAAAGAAAGCGGCTTGCGAGCAACCTTAAATTTGGGTCATACCTTTGGCCATgtaagtagt-ccatgat--ggtctct-----tggacatttcttctc-------------ttcgggcctagatccactcatcaccc--atcactt---aattttgcag------------------------------------------------------------------

upper sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 5
TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtt-atcatgtttggatttttatgtctgattattttttactgtcattgataaggttcgggagcaagaaccttaaccacctttatcacatcaggatt--tatcagaattttggcaaccttatgttattgtaatgcaccaaccatatactgatcctcacagtcgtttgtcag
||||||| |||| ||||||||||| |||||||| ||  |   |||||||||||||||||| ||  | || ||| | ||| ||||||| || |||||||||||  || || |     | || ||  ||||||    |  |||||| || | ||  ||  | || |   ||   |  ||      ||| | | | ||    |||  |||                                                                     
TATCAAGCGATCATGTGAAAACAAGGCTGAGGTAGTATCTTTAGATGAGAAGGAAAGTGGACTGAGGGCGACATTGAACTTGGGTCATACTTTTGGCCATgtgagttttgagttcatgtgaatgattatgt----tctttttttgct-ttataaatctgctt-gttggctttatgctgg--tgcctctcttatatggaaattgctatt--------------------------------------------------------------------

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|32793543|gb|CD945779.1|CD945779
EST:     AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCAT                         GCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTC
genomic: AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTC
EST: gi|32823434|gb|CD963156.1|CD963156
EST:     GGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCGAT                         GCTATCGAGACTGGGACTGCATATGGAGCACGGCTCCATGGGGAGGCTGT
genomic: GGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCC-ATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGT
EST: gi|32793894|gb|CD946130.1|CD946130
EST:     AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCAT                         GCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTC
genomic: AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTC
EST: gi|7031240|gb|AW461128.1|AW461128
EST:     AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCAT                         GCTATCGAGACTGAGACTGGATATGGAGCATGGCTCCATGGGGAAGGCTGT
genomic: AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGA-GGCTGT
EST: gi|32849355|gb|CD989036.1|CD989036
EST:     AGGAAAGTGGCCTACGAGCAACACTTAACCTGGGTCACACATTTGGCCAT                         GCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTC
genomic: AGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTC

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), 48 (downstream exon)
Score: 40

TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTCGCAACTGGAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTCGCAACTGGAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTCGCAACTGGAATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TATCAAGAGATCTTGTGAAAACAAAGCTGAGGTGGTCGCACAAGATGAGAAGGAAAGTGGCCTACGAGCAACACTAAACCTGGGTCACACATTTGGCCATgtatgtgtta ... cgtttgtcagGCTATCGAGACTGGGACTGGATATGGAGCATGGCTCCATGGGGAGGCTGTCGCAACTGGAATA