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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaactaatttacttttggtctcggtcacaacttttctgtcctggtcattcactctgtgctactgatacatagactgcattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA

Basic information

species Zea mays
transcript GRMZM2G031859_T03
intron # 11
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031859_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 3'ss of exon 11
cttcaactaatttacttttggtctcggtcacaacttttctgtcctggtcattcactctgtgctact-gatacatagactgcattccttgacttgagctga---gATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA
  | |  | | ||       |||  | |     |  || | |      ||     | | | ||  | |||    ||| |||||| ||||||| | | |||   ||||| ||||| |||||||| |||||||| |||||||| |||||||||||||| ||  | ||||||||||||||||| ||||||||||| ||||| |||||
--tgatatgaattttcacacgtcatgtttctttcacttttatttcacgcacct--tttatactgtttgatttggagattgcatttcttgactcgggatgactagATATTGCTGACGTCACTAACTTTGTTCATCCTGGTACTCCTCTTGATGAGGAGGCCTCACAAAGGGGCACTTCTGTATATCTTGTTGGACAGCGAATTGA

upper sequence: GRMZM2G031859_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 11
cttcaactaat--ttacttttggtctcggtcacaacttttctgtcctg---gtcattcactctgtgctactgatacatagactgcattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA
       || |  || ||| | || |   | |    | | ||  | |      | |   || |||  | |   || || |      ||   ||  ||    | |||||| |||||||| |||||||||||| | ||||| || || |||||||| || ||||| |||||||| || ||||| || ||||||| || |||||| ||
-----ggtagtgctttcttctagtgtgcatgaattgtatactaacgtatgaagcttatgctatgtaatccctctatatggttcatctttaatggatttctgtcagATATTGCTGATGTGACTAATTTTGTTTATCCTGGCACTCCCCTTGATGATGAGGCTGCACAAAGGGGTACGTCTGTCTACCTTGTTGAGCGGCGGATAGA

upper sequence: GRMZM2G031859_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA06G14870.2 (Glycine max), 3'ss of exon 11
----cttcaactaatttacttttggtctcggtcacaacttttctgtcctggtcattcactctgtgctactgatacatagact-gcattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA
    |||||||  |   |   ||  | |   |  | ||  |  |  ||| |    | |  || |   |    |  ||||  |    ||   ||| ||    | |||||| |||||||| || ||||||||||| ||||| || || |||||||| || ||||| |||||||| || ||||| || ||||||| || |||||| ||
tcctcttcaac--agccaagcttcatttgtttttctaccctcttcccctag---cttatgctatctaatccctctataggttcatctttaatgaatttctgtcagATATTGCTGATGTGACAAATTTTGTTCATCCTGGCACTCCCCTTGATGATGAGGCTGCACAAAGGGGTACATCTGTCTACCTTGTTGAGCGGCGGATAGA

upper sequence: GRMZM2G031859_T03 (Zea mays), 3'ss of exon 11
lower sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 11
cttcaactaatttacttttggtctcggtcacaacttttctgtcctggtcattcactctgtgctactga-tacatagactg-cattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA
||   | |   |||   || ||     |||   | || |   |    || | ||  ||    ||  || |  | |   |    ||   |||  |    | ||| || |||||||| || ||||||||||||||||| || || |||||||| || ||||| ||||||||||| ||||| || ||||||| ||   | |||||
ctggcattggcttatgctttgttct--tcatgtcattccaaactacttcttacaagcttcagtatggagtttacatgttaatctttaatgatatttaatcagACATTGCTGATGTAACAAATTTTGTTCACCCTGGCACTCCCCTTGATGACGAGGCTGCCCAAAGGGGCACATCTGTCTACCTTGTTGAGCGCAGAATTGA

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|32804422|gb|CD956658.1|CD956658
EST:     TGCTCTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTC                         ATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGG
genomic: TGCACTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTCgtatccttga ... ttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGG
EST: gi|211281344|gb|FL440107.1|FL440107
EST:     TGCACTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTC                         ATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGG
genomic: TGCACTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTCgtatccttga ... ttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGG
EST: gi|32804712|gb|CD956948.1|CD956948
EST:     TGCACTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTC                         ATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGG
genomic: TGCACTACATTGCACACTACTTCCAAATGGGAACTTTGAAGTTGGAGTTCgtatccttga ... ttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcattcactctgtgctactgatacatagactgcattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA
                                    ttccttgac  putative branch site 
                      atacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcaactaatttacttttggtctcggtcacaacttttctgtcctggtcattcactctgtgctactgatacatagactgcattccttgacttgagctgagATATCGCTGATGTCACTAATTTTGTTCACCCTGGTACCCCTCTTGATGAGGAAGCTGCGCAAAGGGGCACTTCTGTTTATCTTGTTGGGCAGCGGATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- -caactaa
- - - - - - - -ttttggt
- - - - - - - - - - - - - - - - - - - -tgtcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc