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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgtcacttttgtatggtttagtgttctatcccacatctttttatcagaattgttgtgcactaatggtctttctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG

Basic information

species Zea mays
transcript GRMZM2G101413_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 3'ss of exon 4
gtaagt-tgtcacttttgtatggtttagtgttctatcccacatctttttatcagaattgttgtgcactaatggtctttctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG
|||||    |  |  | ||||| ||  || |  |||||||  | | | |||  |||  |  || |  | | | ||| | |||| |||||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||||||
gtaagcgcctgcccctcgtatgcttgtgtttcatatcccatgt-tctatatatgaaaagaagttc--tgacgatctgtttcttccagCTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAG

upper sequence: GRMZM2G101413_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G12570.1 (Glycine max), 3'ss of exon 4
gtaagttgtcacttttgtatggtttagtgttctatcccacatct-ttttatcagaattgttgtgcactaatggtctttctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG
||||             || |   || | |   ||   |  ||    ||| ||  ||  |         || || || || || |||| ||     | ||| | || || |||||| |||||||||||||||| |||||||||||| | ||
gtaataaaggctgaaaataagaactactttgaaattatatgtcaaccttagcaatatcctgacttctatattgttttactattacagCCTGTGCCTCAGGTGTTGTTCAGACAGCTTTGTATGCAGATTTCTTCTACTATTATTTCATCAG
















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:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|76914884|gb|DV165734.1|DV165734
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGGTGCAA-CAGCTCTGTATGCAGATTTCTTTTAC
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGG-TGCAAACAGCTCTGTATGCAGATTTCTTTTAC
EST: gi|12971772|gb|BG267650.1|BG267650
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|71332207|gb|DR803027.1|DR803027
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|76014786|gb|DT941956.1|DT941956
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|71332206|gb|DR803026.1|DR803026
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTATT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|18181443|gb|BM382653.1|BM382653
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|101390410|gb|EB817139.1|EB817139
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTATT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|113702315|gb|EE679819.1|EE679819
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGTTGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|211107241|gb|FL370796.1|FL370796
EST:     AACTGGATTTATCNGT-ATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCA
genomic: AACTGGATTTATC-GTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCA
EST: gi|71316813|gb|DR795094.1|DR795094
EST:     AGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|18180216|gb|BM381426.1|BM381426
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|60346227|gb|DN213200.1|DN213200
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|211009339|gb|FL418571.1|FL418571
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGNTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|76012114|gb|DT939284.1|DT939284
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|60348027|gb|DN215000.1|DN215000
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|211407829|gb|FL480469.1|FL480469
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|149082455|gb|EE171645.2|EE171645
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|50332292|gb|CO527418.1|CO527418
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|148943936|gb|EC889016.2|EC889016
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|74243070|gb|DT650984.1|DT650984
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|4647085|gb|AI622160.1|AI622160
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|67014344|gb|CO443093.1|CO443093
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|60358513|gb|DN225486.1|DN225486
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|148943937|gb|EC889017.2|EC889017
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|9743078|gb|BE519226.1|BE519226
EST:     AACTGGATTTATCGTTATTTCCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AACTGGATTTATCGTTATTT-CACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|76012125|gb|DT939295.1|DT939295
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|148990937|gb|EE032363.2|EE032363
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCC                         CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACT
EST: gi|101390412|gb|EB817140.1|EB817140
EST:     AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAAATGGATCC                         CTTTGG-TTGCTGGTTTGGTGGAAACAGCT
genomic: AAACTGGATTTATCGTTATTTCACGGAGGGTCATCGCAGCAGATGGATCCgtaagttgtc ... tctctttcagCTT-GGCTTGCTGGTTTGGTGCAAACAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcccacatctttttatcagaattgttgtgcactaatggtctttctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG
                                cactaat  putative branch site (score: 2)
                                      tggtctttctctttc  CT-rich tract
            tttttatcagaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgtcacttttgtatggtttagtgttctatcccacatctttttatcagaattgttgtgcactaatggtctttctctttcagCTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG

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