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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttgagttgttttgaatacttcaaggatcgtttcctagttgtaactgtgttaaaattctttactctttcgaataatatttgctggttggtgagttccttaatagtcagataccttttatatactgctgtgacatttaggtcttaaaacttactacctgtaatcattccattttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATAGTTCGTATCAAGGTACTGCGTAATAAACCAGATCATGCTCTTGTTGAGA

Basic information

species Zea mays
transcript GRMZM2G070113_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070113_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 3'ss of exon 13
gtaagccttgagttgttttgaatacttcaaggatcgtttcctagttgtaactgtgttaaaattctttactctttcgaataatatttgctggttggtgagttccttaatagtcagataccttttatatactgctgtgacatttaggtcttaaaacttactacct--gtaatcattccattttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATAGTTCGTATCAAGGTACTGCGTAATAAACCAGATCATGCTCTTGTTGAGA
                                                                            |     || |||    |  | || |  | ||         | ||||| |  |  | ||| ||     || |||||| |||   | ||  ||  | |   ||| | |  ||||||||||  |||| |||||||| ||||||||||| ||  | || || |||||||| || |||||  ||||||| || ||||||||||| || |||||||| |
---------------------------------------------------------------------------aagcctgatatgccaacttataaggtattcaa---------agcttttgtgcaa-gatgttact----ggccttaaaccttggcatcttagttcttaactcatctgccttgcagAAAATAAATGAAGATAAGCTTTTCAATCTGTTCTCTCTATATGGGAACATAGTCCGAATCAAAATACTGCGCAACAAACCAGATCACGCCCTTGTTGAAA
















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|67016395|gb|CO445144.1|CO445144
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|211376275|gb|FL144037.1|FL144037
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|30031872|gb|CB833723.1|CB833723
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|61118021|gb|DN558982.1|DN558982
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|113701814|gb|EE679318.1|EE679318
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|211376276|gb|FL144038.1|FL144038
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|71436418|gb|DR817468.1|DR817468
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|76011812|gb|DT938982.1|DT938982
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
EST: gi|32915229|gb|CF020041.1|CF020041
EST:     CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGAT                         AAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA
genomic: CTGGTACCAATGAACGGTGCACACTCATAGTCAGTAATCTGAATAATGATgtaagccttg ... ttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgacatttaggtcttaaaacttactacctgtaatcattccattttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATAGTTCGTATCAAGGTACTGCGTAATAAACCAGATCATGCTCTTGTTGAGA
                   aacttac  putative branch site (score: 2)
                                   tcattccattttct  putative PPT
               ttaaaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccttgagttgttttgaatacttcaaggatcgtttcctagttgtaactgtgttaaaattctttactctttcgaataatatttgctggttggtgagttccttaatagtcagataccttttatatactgctgtgacatttaggtcttaaaacttactacctgtaatcattccattttctgtgcagAAAATTGATGAGGATAAGCTCTTCAATCTGTTTTCCTTGTACGGAAACATAGTTCGTATCAAGGTACTGCGTAATAAACCAGATCATGCTCTTGTTGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA