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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGGCATGACGCGTTGCTTTCAGTTCATCCGACAACAGCAGTAGCTTCTAATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccgatcatgcaccattttctttcagaacggtggtatgcagcctcttacagaattctatccttactaaaacag

Basic information

species Zea mays
transcript GRMZM5G834205_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 5'ss of exon 9
---TCCGGCATGACGCGTTGCTTTCAGTTCATCCGACAACAGCAGTAGCTTCTAATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccgatcatgcaccattttctttcagaacggtggtatgcagcctcttacagaattctatccttactaaaacag
   | |||||||| ||||||||||||||||| || || ||| |||||||||||| | | ||||| |||||||| |||||   ||| ||||| || || |||||||| |     || | |   ||||  |     |  ||||| | |  |||  ||||  |||| |  ||| || || ||||
TTGTACGGCATGATGCGTTGCTTTCAGTTCAGCCAACTACAACAGTAGCTTCTACTCTCAAGGAGGAAGAGGAAGAAGA---TGCCGAAAGCCTTTACCGGAGgtatgtgtattcgttctttatttcttc----agtggtggaaggtggccaattactaaatttt--cctcaccaacacag
















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|101391432|gb|EB817651.1|EB817651
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|211390577|gb|FL303486.1|FL303486
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|78077690|gb|DV506124.1|DV506124
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|149050347|gb|EE155591.2|EE155591
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|84970062|gb|DW468434.1|DW468434
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|37375076|gb|CF623952.1|CF623952
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCACTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|71302875|gb|DR787549.1|DR787549
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|71761883|gb|DR959820.1|DR959820
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|86472430|gb|DY238800.1|DY238800
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|48690727|gb|CO049262.1|CO049262
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCACTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|50325059|gb|CO520185.1|CO520185
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|211390578|gb|FL303487.1|FL303487
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|37394180|gb|CF634361.1|CF634361
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCACTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
EST: gi|76291817|gb|DV031385.1|DV031385
EST:     AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAG                         ACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC
genomic: AATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccga ... actaaaacagACTGCGGAAGGGGAAGGCGCTGTCGCAGGACTACACAGATGACCTGGTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGGCATGACGCGTTGCTTTCAGTTCATCCGACAACAGCAGTAGCTTCTAATATAAAGGAAGAAGAGGAGGAAGAGGATGCTGAAAGTCTCTATCGGAGgtaggaccgatcatgcaccattttctttcagaacggtggtatgcagcctcttacagaattctatccttactaaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG