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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTCTTGCATACAGTGATGGGATTAGACCAGTCGAGCCAGCAAGAATGGCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctagaaggcgaataagaattatacaatggttgtaggatttcttttaaatattttttgttgatctgcccccaactttgcttggggtctaaaagaagctttgttgttatatgaatctatatgttatttttttcttacacttgcatttttttag

Basic information

species Zea mays
transcript GRMZM2G053531_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053531_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 8
GAAGTCTTGCATACAGTGATGGGATTAGACCAGTCGAGCCAGCAAGAATGGCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctagaaggcgaataagaattatacaatggttgtaggatttcttttaaatattttttgttgatctgcccccaactttgcttggggtctaaaagaagctttgttgttatatgaatctatatgttatttttttcttacacttgcatttttttag
|||| ||||||||||||||||| || ||| ||||||||||||||||||||||  || |||| ||| | || || |||||||| |||||||| ||||||||||||| |    |     ||     | ||  |  ||||| | |||  |    ||       |||||   |    |     ||  |||   ||||        ||   || | | ||                                         
GAAGCCTTGCATACAGTGATGGCATAAGATCAGTCGAGCCAGCAAGAATGGCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAGgtattgttatggaaatcta-----tttatgactgttgttgaattcat---gaaagcacaatgttgcagtagtactggaattctttgt--tctac------tttcactggtttgtgc----------------------------------------
















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|74035418|gb|DT535906.1|DT535906
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|6695554|gb|AW288662.1|AW288662
EST:     GCAGTAGCAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|84969850|gb|DW468264.1|DW468264
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|60358119|gb|DN225092.1|DN225092
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|211437854|gb|FL220477.1|FL220477
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|78109883|gb|DV528299.1|DV528299
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|12968885|gb|BG265726.1|BG265726
EST:     GCAGTAGCAGCTGGCCTATCAGATGGGGTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|60341680|gb|DN208653.1|DN208653
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|88754483|gb|DY538624.1|DY538624
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|113702906|gb|EE680410.1|EE680410
EST:     GCAGTAGCAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|60394174|gb|DN227044.1|DN227044
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|116822203|gb|EC865582.1|EC865582
EST:     AGATGGG-TGTTA-TTACAGAGCTTGACAG                         A-CTGATGGACAGCCATGTGTGGAGGCTC-AGAGTTTGGACTGGTGAGGAA
genomic: AGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|32846823|gb|CD986504.1|CD986504
EST:     GCAGTAGCAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|6828185|gb|AW331828.1|AW331828
EST:     GCAGTAGCAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|60359057|gb|DN226030.1|DN226030
EST:     GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
EST: gi|78021679|gb|DV490066.1|DV490066
EST:     GCAGTAGCAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAG                         ACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA
genomic: GCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctaga ... atttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGTCTTGCATACAGTGATGGGATTAGACCAGTCGAGCCAGCAAGAATGGCAGTAACAGCTGGCCTATCAGATGGGTTGTTATTTACAGAGCTTGACAGgtattctagaaggcgaataagaattatacaatggttgtaggatttcttttaaatattttttgttgatctgcccccaactttgcttggggtctaaaagaagctttgttgttatatgaatctatatgttatttttttcttacacttgcatttttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT