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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcgtaccattgtgaaatgtcacataccgttaaaatctatcatcatatttcttttttttacttattattgatgctttcatttcgatcattgcag

Basic information

species Zea mays
transcript GRMZM2G101413_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101413_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcgtaccattgtgaaatgtcacataccgttaaaatctatcatcatatttcttttttttacttattattgatgctttcatttcgatcattgcag
||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||||||||||  |||  |||| |||  |||  | |    | | |||                      ||   || |||   || ||| ||| |  ||||||
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttgc----agactct----------------------ctgggtactgacaattccatgtcggttgttgcag

upper sequence: GRMZM2G101413_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G29410.1 (Glycine max), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcgtaccattgtgaaatgtcacataccgttaaaatctatcatcatatttcttttttttacttattattgatgctttcatttcgatcattgcag
||||  |  | ||| | || || |||||| |||||||||||||||| |||||||| ||| | ||||||          |||||    | || |||   |||        | |  ||| |  |  |   ||  || |||       ||  ||| |          
CTTGTGTCTCAGGTGTTGTTCAGACAGCTTTGTATGCAGATTTCTTCTACTATTACTTCATCAGgtaa------cgatattgtccgttttc-catcttgttt-------ttactatactcataataaataggtaatataaggagctttgttttgcag-------

upper sequence: GRMZM2G101413_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G12570.1 (Glycine max), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcgtaccattgtgaaatgtcacataccgttaaaatctatcatcatatttcttttttttacttattattgatgctttcatttcgatcattgcag
| ||     | ||| | || || |||||| |||||||||||||||| |||||||||||| | ||||||  |   ||   |     || |||  ||   |||    | |||  ||||||  |       |   || |||      |||  ||| |          
CCTGTGCCTCAGGTGTTGTTCAGACAGCTTTGTATGCAGATTTCTTCTACTATTATTTCATCAGgtaatgt---tattgtctgttaaggtcg-atcttgtttttgt-tatgctcatataacaaa----tgggtaatataaggagttttgttttgcag-------

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|149082454|gb|EE171644.2|EE171644
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|76914884|gb|DV165734.1|DV165734
EST:     TGGGTGCAA-CAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TGG-TGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|12971772|gb|BG267650.1|BG267650
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|71332207|gb|DR803027.1|DR803027
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|76014786|gb|DT941956.1|DT941956
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|71332206|gb|DR803026.1|DR803026
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTATTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|18181443|gb|BM382653.1|BM382653
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|88753295|gb|DY537436.1|DY537436
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTATTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|101390410|gb|EB817139.1|EB817139
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTATTATTATTTTTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|113702315|gb|EE679819.1|EE679819
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|71316813|gb|DR795094.1|DR795094
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|18180216|gb|BM381426.1|BM381426
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|60346227|gb|DN213200.1|DN213200
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|76012114|gb|DT939284.1|DT939284
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|60348027|gb|DN215000.1|DN215000
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|211407829|gb|FL480469.1|FL480469
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|149082455|gb|EE171645.2|EE171645
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|50332292|gb|CO527418.1|CO527418
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|148943936|gb|EC889016.2|EC889016
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|74243070|gb|DT650984.1|DT650984
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTT
EST: gi|4647085|gb|AI622160.1|AI622160
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|67014344|gb|CO443093.1|CO443093
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACANTGTGAAGCTCGAGTTGCCTGCTTGAGCATGNCT-CGTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATG-CTTCGTTT
EST: gi|60358513|gb|DN225486.1|DN225486
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         T-GGAAGAACA
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACA
EST: gi|148943937|gb|EC889017.2|EC889017
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|9743078|gb|BE519226.1|BE519226
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|76012125|gb|DT939295.1|DT939295
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTTT
EST: gi|148990937|gb|EE032363.2|EE032363
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcg ... atcattgcagTTGGAAGAACAATGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtaaactgcgtaccattgtgaaatgtcacataccgttaaaatctatcatcatatttcttttttttacttattattgatgctttcatttcgatcattgcag

- - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - -  GCAGAT