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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgctaatgtctctcttgtattttaaataggcgtaactagcatttgattgatggctctcgactcctgacaggatccctttgtttatctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTTACTGCACTTGAAGCTATG

Basic information

species Zea mays
transcript GRMZM2G143602_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 3'ss of exon 8
gtgtgtgctaatgtctctctt---gtattttaaataggcgtaactagcatttgattgatg-gctctcgactcctgacaggatccctttgtttatctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTTACTGCACTTGAAGCTATG
|| | | | | || | ||  |   |   ||   | |   ||| |||   |   ||| | |   |   |  |    ||| |||  |||| | ||| |   |||||||| |||||||||||||||||| | || |||||||| ||||| || |||||||||| ||||||||||
gtattt-ccagtgccccttcttcagaggttatcacaaatgtacctactgtc--attaaagtattaatggttttcaacatgatttcttt-tctatgt---tagGCCATCGATTTCCTTGACAAGCTTCTTCGCTATGATCACCAGGATAGACTTACTGCACGTGAAGCTATG
















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|61117728|gb|DN558689.1|DN558689
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|33103216|gb|CF063176.1|CF063176
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|60396112|gb|DN228981.1|DN228981
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|4680837|gb|AI629507.1|AI629507
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|71770652|gb|DR968589.1|DR968589
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|16377160|gb|BI991802.1|BI991802
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|60395786|gb|DN228656.1|DN228656
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|60343609|gb|DN210582.1|DN210582
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|29576767|gb|CB616879.1|CB616879
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|60340369|gb|DN207342.1|DN207342
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|211466861|gb|FL187159.1|FL187159
EST:     CCTGGT-AAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACCAGCTTTTGGCGTTATGATCATCAGGAGAGGCT
genomic: C-TGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTG-CGTTATGATCATCAGGAGAGGCT
EST: gi|113703875|gb|EE681379.1|EE681379
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|78073838|gb|DV502272.1|DV502272
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|60395745|gb|DN228615.1|DN228615
EST:     CCTGGTTAAAGTTTATGAATGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
EST: gi|16379175|gb|BI992806.1|BI992806
EST:     CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAG                         GCCATAGATTTCCCTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT
genomic: CCTGGTTAAAGTTTATGAACGCAGATAACCAGCACCTAGTGTCTCCTGAGgtgtgtgcta ... atctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttgattgatggctctcgactcctgacaggatccctttgtttatctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTTACTGCACTTGAAGCTATG
                       tcctgac  putative branch site (score: 2)
                                  tccctttgtttatctc  putative PPT
                                      tttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgctaatgtctctcttgtattttaaataggcgtaactagcatttgattgatggctctcgactcctgacaggatccctttgtttatctctgtagGCCATAGATTTCCTTGACAAGCTTTTGCGTTATGATCATCAGGAGAGGCTTACTGCACTTGAAGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC