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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgtagcttttcaaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta...

Basic information

species Zea mays
transcript GRMZM2G038791_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 5'ss of exon 3
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgt-----agctttt------caaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta
|||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| || |||||||||||||||||||||     ||||     |  ||||      |||||| | ||| ||||||   | |  |||| | |    |   |     ||||||||||||||||          
TATGGAACTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATTACTGCAGTCATCCCTTATTTTGGTTATGCCAGAGCTGACAGGAAGgtaatgttgtcaacttgtcatacaattttttgcctccaaattatcttagtggttttgggatcattttattttttgag--tggcatttgtcacatgcttgtaa---------

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G12660.1 (Glycine max), 5'ss of exon 3
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaa---tgttgctttattgtagcttttcaaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta
|||||||||||| || |||||||||||||| ||||| || || || || ||||| ||||| || || || |||||||| ||||| || ||||| || |||||     |||    |||     || |||  | || || |    | |  ||  ||||  ||  |     |   |     | || || ||||||           
TATGGAGCTTCTCATAATGATTGATGCCTGCAGGAGGGCTTCAGCCAAAAATATTACTGCTGTCATTCCGTATTTTGGATATGCCAGAGCTGATAGAAAGgtctgcttgtcagcttacgtatgcatttatatttattatttctgatgaaattttgtccttcctattccac-catattctatcccaggcttgtcttgaaatt--

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G06110.1 (Glycine max), 5'ss of exon 3
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgtagcttttcaaattgttttaatggtttcaaggttgtt--ttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta----
 |||||||||   || ||||||||||| ||| |||||||||| || |||||||||||||| || || || || ||||| ||||| || ||||| || |||| || ||   ||     || || ||    ||  |||  |   ||     ||| |  ||||||  ||  | | || | | | |    |   | | | | |  |    
CATGGAGCTTAAAATAATGATTGATGCTTGTCGGAGAGCATCCGCCAAGAATATCACTGCTGTGATTCCCTACTTTGGATATGCCAGAGCTGATAGAAAGgcaa-gtattttggacataactgtt----tttcttttgtatctttgtaattggtagttttattcaaggagt-ctacctatgatccacaattgctattgcagacaat

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G24280.2 (Glycine max), 5'ss of exon 3
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgtagctt--ttcaaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta
|||||||||||| || |||||||||||||| ||||| || || || || ||||| ||||| || || || |||||||| ||||| || ||||| || |||||    |||     ||  |  |   || | ||| | ||| |  |    | ||| | |  |    |    |   |  |   | || ||||||           
TATGGAGCTTCTCATAATGATTGATGCCTGCAGGAGGGCTTCAGCCAAAAATATTACTGCTGTCATTCCATATTTTGGATATGCCAGAGCTGATAGAAAGgtctgtttgtcagcttacatatgcatttatatt-tattatttctgatgaagttttgtccttcttattccaccatattctccccaggcttgtcttgtaattg-

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 5'ss of exon 2
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttat----tgtagct--tttcaaattgttttaatggtttcaaggttgtttt-ttatggaaaaaatactgcttgtcacat-gcttgtaccactccgta---
 ||||||||| |||| ||| | ||||| ||  | |||||||| ||||||||  | || || || || || |||||||| |||||||| |||||||||||||||| ||  |||| |    | |||||  ||||| ||  | |  | |||||   | |   ||   ||| |  ||  |  |     | | || |  |||    || | |    
CATGGAGCTTTTGATTATGGTAGATGCTTGCCGAAGAGCATCAGCTAAGAAAGTTACAGCTGTGATTCCGTATTTTGGATATGCAAGAGCTGACAGGAAGgtaaagtctctttgtgtggtttagctactttcacatgatatggagggtttgttgataacttagctattggtaatcttttctggataaaattgtatgttttgctgcttgcag

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G44530.2 (Arabidopsis thaliana), 5'ss of exon 3
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgtagcttttcaaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta-----
||||||  | ||  | ||||||||||| ||| |||||||||| || || | |||||| || || || ||||| |||||||||||| | ||||| || |||| ||   |  |||  | || || |  ||  ||| ||   || |||||   |  | |  |   |   |  |    ||||| |        | |  |    |     
TATGGAATTGCTCGTTATGATTGATGCTTGTCGGAGAGCATCAGCCAAAACTATCACGGCTGTGATTCCTTACTTTGGTTATGCACGAGCTGATAGAAAGgcaa--gtctttttctataactatagaatctgtctt---ggattcaatcgtcctgtgaaaacatgcacaatgatttgtctccaagagtaatcgattgtcagttta

upper sequence: GRMZM2G038791_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 5'ss of exon 3
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgtagcttttcaaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta------
 ||||||||| |||| ||||| ||||||||| |||||||||| || || ||||||||||| || || || |||||||| ||||| || ||||| || |||||||  |   |   |||| |  |   |     |  |   | ||||||  ||| |   |    |||||         |  |||   ||| || | |  |        
AATGGAGCTTTTGATAATGATAGATGCCTGTCGGAGAGCATCAGCCAAAAATATCACTGCTGTGATTCCATATTTTGGATATGCCAGAGCTGATAGAAAGgtaac-tccttcatttgtggtataagaggaactcgttcagatttcaaaattgatgcctgaaaaaaaaggg-----ggggacagatttggacaaatttgaggtgatt

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|211126323|gb|FL371824.1|FL371824
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|76014853|gb|DT942023.1|DT942023
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|211452034|gb|FL391255.1|FL391255
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|148941796|gb|EC886762.2|EC886762
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|71429936|gb|DR810986.1|DR810986
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|76914467|gb|DV165542.1|DV165542
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|94476090|gb|EB705048.1|EB705048
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|78118884|gb|DV537268.1|DV537268
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGAAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|91052224|gb|EB162642.1|EB162642
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|78120522|gb|DV538906.1|DV538906
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|211341635|gb|FL411914.1|FL411914
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|71771273|gb|DR969210.1|DR969210
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|149077159|gb|EE165820.2|EE165820
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|74243300|gb|DT651214.1|DT651214
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|148965187|gb|EE015993.2|EE015993
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|101391941|gb|EB817900.1|EB817900
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|31354058|gb|CD438415.1|CD438415
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|148931525|gb|EC874574.2|EC874574
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|26457160|gb|CA828743.1|CA828743
EST:     TTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: TTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
EST: gi|101393322|gb|EB818592.1|EB818592
EST:     ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAG                         TCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC
genomic: ATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgc ... tttttttcagTCCCAGGGCAGGGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGAGCTTCTGATCATGATTGATGCCTGTAGGAGAGCATCTGCTAAGAATATCACTGCAGTTATCCCTTATTTTGGTTATGCAAGGGCTGACAGGAAGgtaatgttgctttattgtagcttttcaaattgttttaatggtttcaaggttgttttttatggaaaaaatactgcttgtcacatgcttgtaccactccgta

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