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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACATTGTCGACGTAAGCTCATATGGCGAGCTGAAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaactttggtaaacatattcgttctcatgtttgtactgtataagtatagcacacgccagttgtttccatggcacatgttaaatttttactgaactctggcaaacttcag

Basic information

species Zea mays
transcript GRMZM2G107089_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107089_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 5'ss of exon 8
TAACATTGTCGACGTAAGCTCATATGGCGAGCTGAAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaactttggtaaacatattcgttc--tcatgtttgtactgtataagtatagcacacgccagttgtttccatggcacatgttaaatttttactgaactctggcaaacttcag
|||||| || || |||||||||||||| || |||||||| || ||| | || || || ||||| ||||| || |||||||||||||||||  | |||        | || || |     ||||  |  | | | |   |    ||  |  | |   |   ||| | |  | |                             
TAACATAGTTGATGTAAGCTCATATGGAGAACTGAAGGAGGCCATTGCCGAGGGTAAATGGGCGAGAGGGCCATGGTCAGCTAGgtaggtgcagtttaaatgcgctgtttgtccaacagtgttaatgttattttatgtttttgcaaacttgattcatttgtggtatacttcag----------------------------

upper sequence: GRMZM2G107089_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 5'ss of exon 10
TAACATTGTCGACGTAAGCTCATATGGCGAGCTGAAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaactttggtaaacatattcgttctcatgtttgtactgtataagtatagcacacgccagttgtttccatggcacatgttaaatttttactgaactctggcaaacttcag
||||||||| || || ||||| ||||  |||||||| || || |||||| | ||||| ||||| || ||||||||||| ||||||||  |||| |||| |     | ||   |   || ||||     |  || | ||  | | || ||| |||||   |||   | |  | || ||  |  |                
TAACATTGTGGATGTCAGCTCCTATGATGAGCTGAAAGAGGCCATTTCTCAGGGAAAATGGGCAAGGGGTCCTTGGTCGGCTAGgta--ttaaatttgtt-----tctttcattgtatttttgactcatccaact-ta--atatgctagt-gtttctgaggccattctccatttgttggtatag---------------
















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|211038835|gb|FL468655.1|FL468655
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|4646967|gb|AI622042.1|AI622042
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|32832964|gb|CD972642.1|CD972642
EST:     AAGGAAGCTATTTCTGAAGGAAAATGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|32833724|gb|CD973402.1|CD973402
EST:     AAGGAAGCTATTTCTGAAGGAAAATGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|32834986|gb|CD974664.1|CD974664
EST:     AAGGAAGCTATTTCTGAAGGAAAATGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|5006223|gb|AI712285.1|AI712285
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCCCCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|148962200|gb|EE013015.2|EE013015
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|76018747|gb|DT945917.1|DT945917
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|60397373|gb|DN230189.1|DN230189
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|32864246|gb|CF003928.1|CF003928
EST:     AAGGAAGCTATTTCTGAAGGAAAATGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|83279137|gb|DV943145.1|DV943145
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|32835396|gb|CD975074.1|CD975074
EST:     AAGGAAGCTATTTCTGAAGGAAAATGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|148954704|gb|EC900156.2|EC900156
EST:     AAGGAAGCTATTTTTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|33091118|gb|CF051112.1|CF051112
EST:     AAGGAAGCTATTTCTGAAGGAAAATGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|149110508|gb|EE190454.2|EE190454
EST:     AAGGAAGCTATTTTTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCCCCATCAGATG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTGAAAGAAGAGACCAGCGCCACCATCAGATG
EST: gi|166641281|gb|EG143648.1|EG143648
EST:     AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAG                         CGATGCTGATGAGCTGAAAGTG
genomic: AAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaac ... caaacttcagCGATGCTGATGAGCTGAAAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACATTGTCGACGTAAGCTCATATGGCGAGCTGAAGGAAGCTATTTCTGAAGGAAAGTGGGCTAGAGGTCCTTGGTCAGCTAGgtaggttaactttggtaaacatattcgttctcatgtttgtactgtataagtatagcacacgccagttgtttccatggcacatgttaaatttttactgaactctggcaaacttcag

- - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT