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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag

Basic information

species Zea mays
transcript GRMZM2G083716_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctg-tttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
|||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| ||||| ||||||||| ||||||| || ||||||||||||||| ||  |     ||||    ||   |  |  | | ||||| |||| |   || | |||||  |    |  |      |     | ||  |                                                                                         
TCTCTATGTTGTGGAGGGAATGCAGTTTGAACGTGGTTATATCTCCCCGTATTTTGTAACTGACAGCGAGAAAATGTCTGCAGAATATGAGAACTGCAAGgtagcttcag--cctgagcacacatacccctgctgtatgctgctttaatctgtttcagtttcttattgcactatgtttccactatttttcag-----------------------------------------------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
||| |||||||| ||||| |||||||||||||||||||| || ||||| |||||||| || ||||||||||||||| | |  || || |||||||| ||||    ||| | || ||   | |   |||  | |   ||| | ||  ||  |  | |  |||| |   ||  | ||  |   || |  |  |   ||  |                                                                                 
TCTATATGTTGTCGAGGGGATGCAATTTGACCGTGGTTATATTTCTCCATACTTTGTTACTGACAGTGAGAAAATGGCCGTTGAATATGAGAACTGTAAGg----tgtgacatttg---tctgttttccctgtaacttgttattattttttaacatccttcatatttaattataacttt--acatggtatgttatgcag---------------------------------------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
||| |||||||| ||||| |||||||| ||||||||||| || ||||| ||||| || || ||||||||||||||| |||  ||||| |||||||| ||||| |     | || ||   | |   |||  |     ||  | ||| ||    |||||| |    |   | |      | ||   | ||  |  |                                                                                      
TCTGTATGTTGTTGAGGGGATGCAATTCGACCGTGGTTATATTTCTCCATACTTCGTTACTGACAGTGAGAAAATGGCTGTTGAGTATGAGAACTGTAAGgtga----gacatttg---tctgttttccctgcgaattattattttttaacatcctgtgtatttacttatagctttatatggtatgttatgcag--------------------------------------------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgta----aaatatgagatatcaattcttttttttttgctgtttattgctttcctg----tttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
 ||||| || || || ||||||||||||||||||||||| |||||||| |||||||| |||||||| ||||||||| | |  |||| ||| || |||||||||  |||      ||| |||| ||  |  |   |||| || || |  ||||      ||     | |  | | |  |  | |||   || || |   |   |||    |   |||                                                                        
CCTCTACGTCGTAGAAGGAATGCAATTTGACCGTGGTTATATCTCTCCTTACTTTGTGACAGACAGCGAGAAAATGTCCGTCGAGTTCGACAATTGCAAGgtagatgtttcttgaatctgag-tagaagatgaattttgttggcagactatttagccactaaagatatttatatatgagtataacaacgatctttaatgttttggtatgattgcag------------------------------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT5G56500.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
 || || ||||| || |||||||||||||| |||||||| |||||||| |||||||| || |||||||||||||||  |||||| || |||||||||||||||    ||   | |      | || ||||  |   |        |  ||  |  | |||    |  | |       |||  | | |||  |                                                                                        
CCTTTACGTTGTTGAAGGAATGCAATTTGATCGTGGTTATATCTCTCCTTACTTTGTCACCGACAGTGAGAAAATGTGTGCAGAATATGAGAACTGCAAGgtattattattgtttatacagttaaatcttaatagctgataaaaaaccgcagtatttttt---gactatatgtctcttcttgctt-ttgtag----------------------------------------------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatat---gagatatcaattcttttttttttgctgtttattgctttcct-gtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
 || ||||||||||| ||||||||||||||||||||||| ||||| || |||||||| |||||||||||||||||| |||  ||||| || || |||||||||| | |    |||   ||| || |||    |  | || || ||   || || |  |  ||||| |  |   |                                                                                                              
CCTTTATGTTGTGGAAGGAATGCAATTTGACCGTGGTTATATCTCCCCATACTTTGTGACAGACAGTGAGAAAATGTCTGTTGAGTATGACAATTGCAAGgtaatttttctttattctgagctaccaaa--atgatattgtgatgcaaatagcctaacaagtttctactgtgcag-------------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 5
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
  | ||||||||||| |||||||| ||||| |||||||| |||||||| ||||| || |||||||||||||||||| |||  || || || || ||||||||||      |     |||  |||    |||||||         ||| |  | |  |     ||| |  |    || | | || | ||   |  |  || |   |     | | |    |    | |   |||  ||   ||  || || ||||                          
CTTGTATGTTGTGGAAGGAATGCAGTTTGATCGTGGTTATATCTCTCCTTACTTCGTCACAGACAGTGAGAAAATGGCTGTTGAATATGAAAATTGCAAGgtaa-----gaggccaagacttcagcattttttttcca------tatagtctccaag----gaaatatgaccctaagtgttacttgttactgactctggtttt-atctcccttcgttttattatattgatttttttgggacat-ctgtttatgcag------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 6
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgt-------aaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag
 || |||||||| || ||||||||||||||||||||||| ||||| || |||||||| || || |||||||||||| | |  || | |||||||||||||||     |       | ||| |  || | | | | |  |  || |||   ||  | |||||  | ||   ||   | |||      | |  ||                                                                                              
CCTGTATGTTGTTGAAGGAATGCAATTTGACCGTGGTTATATCTCACCTTACTTTGTCACCGATAGTGAGAAAATGGCAGTTGAATTCGAGAACTGCAAGgtttgcatttctcttataatttaggagagctaatatggtacttctgcaagttggttctttctggctttctaactgacaaattttgttcatgtag---------------------------------------------------------------------------------------------

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|32849554|gb|CD989235.1|CD989235
EST:     TACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: TACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|211389169|gb|FL356628.1|FL356628
EST:     AGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: AGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|211390791|gb|FL311861.1|FL311861
EST:     GAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
genomic: GAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|32849394|gb|CD989075.1|CD989075
EST:     TACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: TACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|32924519|gb|CF029331.1|CF029331
EST:     ACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: ACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|87156784|gb|DY401573.1|DY401573
EST:     CGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
genomic: CGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|32935129|gb|CF039941.1|CF039941
EST:     TACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: TACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|211072617|gb|FL332508.1|FL332508
EST:     ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|211390788|gb|FL311858.1|FL311858
EST:     ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
genomic: ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|211420404|gb|FL361813.1|FL361813
EST:     GAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
genomic: GAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|51592649|gb|CV071795.1|CV071795
EST:     ACTTTGTAACAGACAGTGAGAANTTGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|211414113|gb|FL317428.1|FL317428
EST:     GAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
genomic: GAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|60343427|gb|DN210400.1|DN210400
EST:     ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|32908575|gb|CF013388.1|CF013388
EST:     ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACC
genomic: ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACC
EST: gi|211429665|gb|FL316454.1|FL316454
EST:     ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAATGCAAGGGATCTTATCAACGTT
genomic: ACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
EST: gi|26558604|gb|CA830839.1|CA830839
EST:     CGAGAACTGCAAG                         CTGCTTTTGGCTT--TAAGAAAATCACCAACGCAAGGGATCTTATCAACGT
genomic: CGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGG-TTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGT
EST: gi|22545873|gb|BU098247.1|BU098247
EST:     CGAGAACTGCAAG                         CTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT
genomic: CGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTT

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), 49 (downstream exon)
Score: 341

TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 872

TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 528

TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaa ... cattgttcagCTGCTTTTGGTTGATAAGAAAATCACCAACGCAAGGGATCTTATCAACGTTTTGGAAGAAGCCATCAGAGGTGCATACCCAATCCTGATAATTGCAGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTATGTTGTGGAGGGAATGCAATTTGACCGTGGTTACATCTCTCCGTACTTTGTAACAGACAGTGAGAAAATGACTGCAGAGTACGAGAACTGCAAGgtaactgtaaaatatgagatatcaattcttttttttttgctgtttattgctttcctgtttcaaaagaaaaaaaaaactctgacctattggggggtgggggtaagacagttcctaggcaaacagcagttgctttcctgtttcagactattaatgctattgtctttcatcttcattgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG