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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagttttgtacctgtgcgtgagttggactacatagggtccttattcctaattgtcatactaattaagaacacatggtcttgtttattttgttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAACGGAAGAACAATGCAATTTGCGGTGGCACCACCAGAAACCCCTATCTCAC

Basic information

species Zea mays
transcript GRMZM2G156734_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g36740.7 (Oryza sativa), 3'ss of exon 6
gtagttttgtacctgtgcgtgagttggactacatagggtccttattcctaattgtca----tactaattaagaacacatggtcttgtttattttgttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAACGGAAGAACAATGCAATTTGCGGTGGCACCACCAGAAACCCCTATCTCAC---
 |   ||||  | ||||| | | |     | || |||||   ||| | ||||| |||    |  || |||  ||||  |    || |||| |||| |   ||||||||||||||||||  ||||||| |||||||| ||||| || || || || ||||| || |||||||| || || || |||   ||| | |||| | |||   
-ttcgtttgagcatgtgcatcattctttat-cacagggta--tatccttaattttcacctgttttatttattaacagtttacattatttactttggtgaatcagGAAGAAGCAATGCTTCTACCAACTGAAGTGGCAATCATACTCCACCGAAATGGAAGGACTATGCAATTCGCCGTAGCGCCA---GAATCTCCTACCACACCTC
















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|33101150|gb|CF061110.1|CF061110
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|60357633|gb|DN224606.1|DN224606
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTTTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|74242886|gb|DT650800.1|DT650800
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|78545094|gb|DV622592.1|DV622592
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|5871396|gb|AW017867.1|AW017867
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|6031346|gb|AW076203.1|AW076203
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32924962|gb|CF029774.1|CF029774
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32924741|gb|CF029553.1|CF029553
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|166528927|gb|EG304034.1|EG304034
EST:     TAGTATCATGCAGCGTCAAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: TAGTATCATGCAGCGTC-AAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|5770167|gb|AI973341.1|AI973341
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32925907|gb|CF030719.1|CF030719
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|78125041|gb|DV543425.1|DV543425
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32925165|gb|CF029977.1|CF029977
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|5325050|gb|AI783241.1|AI783241
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|78074789|gb|DV503223.1|DV503223
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32926687|gb|CF031499.1|CF031499
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|60358023|gb|DN224996.1|DN224996
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|71332392|gb|DR803152.1|DR803152
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|6031347|gb|AW076204.1|AW076204
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32925763|gb|CF030575.1|CF030575
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|16378881|gb|BI992655.1|BI992655
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|86469928|gb|DY236298.1|DY236298
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|211448714|gb|FL094698.1|FL094698
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|5846862|gb|AI999945.1|AI999945
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32926380|gb|CF031192.1|CF031192
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32924716|gb|CF029528.1|CF029528
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|60395273|gb|DN228142.1|DN228142
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|32840136|gb|CD979817.1|CD979817
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGGCAG                         GGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAA
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagG-AAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAA
EST: gi|60336732|gb|DN203705.1|DN203705
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|78021497|gb|DV489884.1|DV489884
EST:     TTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTTTGCATCGGAAC
genomic: TTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
EST: gi|211013250|gb|FL462098.1|FL462098
EST:     ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG                         GAAGAAGCCATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC
genomic: ATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggct ... gttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctaattgtcatactaattaagaacacatggtcttgtttattttgttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAACGGAAGAACAATGCAATTTGCGGTGGCACCACCAGAAACCCCTATCTCAC
            tactaat  putative branch site (score: 1)
                                         ttttgtt  putative PPT
                                  ttgtttattttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttgtacctgtgcgtgagttggactacatagggtccttattcctaattgtcatactaattaagaacacatggtcttgtttattttgttacgtcagGAAGAAGCAATGCTATTACCAACGGAAGTGGCGATCATTCTGCATCGGAACGGAAGAACAATGCAATTTGCGGTGGCACCACCAGAAACCCCTATCTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - gtgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgttt