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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacagtaaaatcattttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

Basic information

species Zea mays
transcript GRMZM2G366935_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 4
ttgacagtaaaatcatt-ttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
 ||    |||||   || | ||||||  ||||| ||||||  |  ||||||   |||||  || |||   ||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
-tgcttataaaacagttgtcgttctttgctcataaaggtttgccgatatggaaacaaatcaaagataatttttcttcaatggatatcgatggttttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 4
ttgacagtaaaatcattttgttcttcactcatgaaggttcc-ctcatatggtcccaaattta--aaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
   | |||  | |  ||||  | |     ||||  ||||    ||||    |    || | |  | | | | |   ||||||| || |  ||| | || |||||| |||||||||||||| |||||||| | |||||||||||||||||||| |||| | || ||||||||||| ||||| ||||| |||||||| || || |
--tatagtgga-ttgtttttatatatgtccatgtgggttttattcatggatttgataactaagcagaaacattcctttcaatgcattttaatggtgttatcagGTCTTTGAGAAGCTTGGACCAAGCTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTCCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: AT4G32660.1 (Arabidopsis thaliana), 3'ss of exon 5
--ttgacagtaaaatcattttgttc-ttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttat-tcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
  |  | |||    |  | | |||  || |||||||  | ||   ||  |  ||    || | ||   |  |||  | | |||| |     ||| |  |  ||||| || ||||||||||||||||| |||| ||| |||||||||||||||| ||||    | || ||| |||  ||||| ||||| |||||| | || || |
cgtgtatagtgt--ttgtgtagtttgtttactcatgtggattttttcgaa--gtttggaactaaacggaaccttcctgtgaatgaactctaatggtgataccagGTGTTCGAGAAGCTTGGGCCAAGTTTGTTTGACTTTCTAAAGAGAAATAAATACTCCGCATTTCCTCTGGCCCTTGTTCGGGATTTTGGATGCCAGCTTT

upper sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 5
ttgacagtaaaatcattttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaat----atactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
       ||   | | ||  ||  || |   || |  |||  ||||| |     ||| |||| ||    ||  |   || |||| |  |  ||| | ||  ||||| |||||||||||||| ||||| || | |||||||||||||||||||| |||| | || || |||||||| ||||| ||||| |||||||| || || |
--tgtgatagtttgaattaatttctc-cctgtggac-ttcattcataagactggaaacttaacattgaaatcttcctttgaatgcactttaatggtgttaccagGTGTTTGAGAAGCTTGGACCAAGTTTATTTGATTTTCTAAAGAGAAATAAATACTGCCCATTTCCTGTGGATCTTGTTCGGGAATTTGGACGTCAGCTTT

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|148983054|gb|EE028963.2|EE028963
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|211042609|gb|FL405101.1|FL405101
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|93015243|gb|EB640763.1|EB640763
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|211070907|gb|FL383766.1|FL383766
EST:     CTGTGTTCAA-TACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGCGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|149000442|gb|EE037616.2|EE037616
EST:     CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
EST: gi|211340986|gb|FL379602.1|FL379602
EST:     CTGTGTTCAA-TACAGAGATGGTTTGACTATCGTAATCATATATGCATT                         GTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA
genomic: CTGTGTTCAAATACAGAGATGGTTTGACTATCGTAATCATATATGCATTgtaagtacta ... attttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT
                                              ttttgtc  CT-rich tract
         aaatttaaaatatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgacagtaaaatcattttgttcttcactcatgaaggttccctcatatggtcccaaatttaaaatatactttattcaatggatatcgatgattttgtcagGTTTTTGAGAAGCTTGGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCGACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGT

- - cagtaaaa
- - - - - - - -ttttgtt
- - - - - - - - - - - - - - -catgaag