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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaatgcatacatatctaatatgctaatcctgcagatttatgtcatccatgtatcgaggttttttcaattctttccttgtccttagctgtggcta...

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 5'ss of exon 6
ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaatgcatacatatctaatatgctaatcctgcagatttatgtcatccatgtatcgaggttttttcaattctttccttgtccttagctgtggcta-----
|||||||||||||||| | || |||||||||||||| ||||||||||| |||||||| || || |||||||||| ||||   | |   | ||||| || | ||||  |||  |    | ||| ||| |||  | |  |||| ||||| ||  | ||  || |   |      
ATACTTCACTGGTCTCTTGTCACCATGGAAAGGCATTTTACTTTTTGGTCCCCCAGGAACTGGGAAGgtttgtatatgcg--cttgattgatatgttacttctgctaattggtcgagtacatctatggag--tatagcaatactttc-ttaccttttcctatatttgaatgc

upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 6
ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaatgcatacatatctaatatgct---aatcctgcagattta-tgtcatccatgtatcg-aggttttttcaattctttccttgtccttagctgtggcta
 ||||||||||||||  | || |||||||| || ||| | ||||||||||| || |||||||||||||||||||   | || |  |||  | ||  |   ||   |||    ||| |||||| |    || | | |    |   ||| | |   ||  |  |  |       
GTACTTCACTGGTCTGTTATCACCATGGAAGGGTATCCTCCTTTTTGGCCCACCGGGGACAGGAAAGgtttgtattggtattc-catcagaaatatttacaacattgcctccttagtgtcattctgaaattgtaagagaatgttattgtgtgggtgcacacaaataaa----

upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G26100.1 (Glycine max), 5'ss of exon 6
ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaatgcat-acatatctaatatgc-taatcctgcagattta-tgtcatccatgtatcg-aggttttttcaattctttccttgtccttagctgtggcta
 ||||||||||||||  | || |||||||| |||||| | ||||||||||| || |||||||||||||||||||   | ||  |||    || ||    |    |||    ||| |||||| |    || | | |    |   ||||| |   ||  | ||  |       
GTACTTCACTGGTCTGTTATCACCATGGAAGGGCATCCTCCTTTTTGGCCCACCGGGGACAGGAAAGgtttgtattggtattgcatcagaaacatttacagcgttgcctccttagtgtcattctgaaattgtaagagaatgttattctgtgtgtgcacgtaaataaa----

upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 5'ss of exon 6
ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaatgcatacatatctaatatgctaatcctgcagatttatgtcatccatgtatcgaggttttttcaattctttccttgtccttagctgtggcta-----
 ||||| |||||||| || || ||||||||||| ||  | |||||||| || ||||| |||||||||||||||       ||||  | | || |  || |  ||  ||    | | ||  || |        ||||| ||| ||||  |  |  ||   | |          
GTACTTTACTGGTCTTCTATCACCATGGAAAGGTATTCTCCTTTTTGGTCCTCCAGGAACAGGAAAGgtttgtgttc---tacaagttttat-tattatttttggtgaacc-ttttatttattttatttttattttttaatgctttattcatgtttccttttcatctcatta

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|148995361|gb|EE034575.2|EE034575
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|91876817|gb|EB406774.1|EB406774
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|166535406|gb|EG282209.1|EG282209
EST:     TGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|211165539|gb|FL456882.1|FL456882
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|149080059|gb|EE169077.2|EE169077
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|211131749|gb|FL468282.1|FL468282
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|32837432|gb|CD977110.1|CD977110
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGAACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|32849820|gb|CD989501.1|CD989501
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGAACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|148963213|gb|EE014191.2|EE014191
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|76281419|gb|DV020987.1|DV020987
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|67021064|gb|CO449813.1|CO449813
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|32838514|gb|CD978192.1|CD978192
EST:     TTCTCCATGGAAAGGGCATCTTACTTTTTGGCCCCCCAGGAACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTCTCCATGGAAA-GGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
EST: gi|22472534|gb|BU037014.1|BU037014
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGT
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGT
EST: gi|31355569|gb|CD439926.1|CD439926
EST:     TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAG                         ACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC
genomic: TTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAAC

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), 48 (downstream exon)
Score: 359

ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 289

ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 254

ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 288

ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaat ... tgttctttagACAATGCTGGCAAAAGCGGTCGCTACTGAGTGCAAAACCACCTTCTTCAACATTTCAGCATCATCAATTGTCAGCAAATGGCGTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATACTTCACTGGTCTCCTTTCTCCATGGAAAGGCATCTTACTTTTTGGCCCCCCAGGGACAGGAAAGgtttgtaaatgcatacatatctaatatgctaatcctgcagatttatgtcatccatgtatcgaggttttttcaattctttccttgtccttagctgtggcta

- - - - - - - - - - -  CATGGA