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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcattatcatctgttgcaaaatgacgatggagtgtttgaggactgatgctcgccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGAGGAAGCTGGAGGAGCAGCAGCAGGCCGCTGCTGCCGAGCTGCAGCAGGC

Basic information

species Zea mays
transcript GRMZM2G311665_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g48410.2 (Oryza sativa), 3'ss of exon 4
gtaaggcatt---atcatctgttgcaaaatgac-----gatggagtgtt--tgaggac---tga---tgctcgc--cgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGAGGAAGCTGGAGGAGCAGCAGCAGGCCGCTGCTGCCGAGCTGCAGCAGGC------
|| ||   ||   |||||||  | ||   |||      ||  || ||||  |||   |   |||   || | |    |  |||||||||||| ||||| ||||||||  |||||||||| ||||||||||||||||||||||||||||||||||||||||||||      |||||||||||||||      
gtgagcttttgcgatcatcttcttcatggtgattgggtgaatgattgttgctgaaatcgcatgagtctgtttgtaatggtgtcagGTGCGAGAATGCTGCAGCACTCCAACAGCGCGAATGAGATGCTGCTGAGGAGGAAGCTGGAGGAGCAGCAGCAGGCCGC------CGAGCTGCAGCAGGCGATCGA
















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|148933686|gb|EC877586.2|EC877586
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATTTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|87157568|gb|DY402357.1|DY402357
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGAA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|149096961|gb|EE182760.2|EE182760
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|88756925|gb|DY541066.1|DY541066
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|148937220|gb|EC881402.2|EC881402
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|149088773|gb|EE177898.2|EE177898
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|22520971|gb|BU079782.1|BU079782
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATG
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATG
EST: gi|71771644|gb|DR969581.1|DR969581
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|148962434|gb|EE013289.2|EE013289
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|148933685|gb|EC877585.2|EC877585
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|149072206|gb|EE160452.2|EE160452
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|149015392|gb|EE045235.2|EE045235
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCCCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
EST: gi|149082408|gb|EE171596.2|EE171596
EST:     CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGG                         GTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA
genomic: CTCCAACGGGTTAGACGGCAGAGAAAACCACTTGGATCTGCACCAGCTGGgtaaggcatt ... ccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctgttgcaaaatgacgatggagtgtttgaggactgatgctcgccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGAGGAAGCTGGAGGAGCAGCAGCAGGCCGCTGCTGCCGAGCTGCAGCAGGC
                                 gactgat  putative branch site (score: 3)
          aaaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcattatcatctgttgcaaaatgacgatggagtgtttgaggactgatgctcgccgccgtcagGTGCGAGGATGCTCCAGCACTCGCACAGCGCGAACGAGATGCTGCTGAGGAGGAAGCTGGAGGAGCAGCAGCAGGCCGCTGCTGCCGAGCTGCAGCAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG