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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttattgtgcttacatgtgtcacctggaatatgtagttcttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG

Basic information

species Zea mays
transcript GRMZM2G366935_T08
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 3'ss of exon 10
-------------gggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttat-tgtgc-ttacatgtgtcacctggaatatgtagttcttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG
                |  |  |||  |  | |  |   |||||  || ||||| || |  | ||  || | ||| |    | ||||| |||||||||| ||||| || |||||||||||||| ||  | | | | ||| ||||||||||||||||||||||||||||||| || |||||||| || || ||||| |||||       
gctatggtatgctaccatttactgtcttgcaatgatcaatcttc--ttcattttatactgattttccatatttgcatcgtgtatgtcaactggaatatgcagTTCATCAGCTCAGAAATATTTTAGACGAGGAGCGCGTCTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAGAGTATCAGAGCAGTCAAAAAACTAGATCGG------

upper sequence: GRMZM2G366935_T05 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 10
---gggaactcttgtaa-tatatttttgtttcttccatttattttctaatattcttt---tattgtgcttacatg----tgt-cacctgga-atatgtagttcttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG
   |   | |  |||   | ||||||||| |    |    |||    |||  | |||   |||    |||  |||    | |  | ||| | || || ||      || | | || ||||||||| | | | |||| || |||||||||||||| || ||||| || ||||| |||||||| |||||||| || || ||       
cttgatcattgctgtccctctatttttgtatgcatctaaaattcgagaatgatgtttcgatatcaccctttaatgccattatatatctgtatatttgcagCCGAAGTGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGAAGGAGCAGTTTCTAGGGAAAGTATCAGAGCAGTGAAGAAGCTTGACCGT------
















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|32832652|gb|CD972330.1|CD972330
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... ttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCA
EST: gi|32834578|gb|CD974256.1|CD974256
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... ttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCA
EST: gi|60356689|gb|DN223662.1|DN223662
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAAGCAAG                         AAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... ttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttttattgtgcttacatgtgtcacctggaatatgtagttcttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG
             tgcttac  putative branch site (score: 2)
                                          ttcttctgctc  putative PPT
     ttttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaactcttgtaatatatttttgtttcttccatttattttctaatattcttttattgtgcttacatgtgtcacctggaatatgtagttcttctgctcagAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGAAGGTGCTGTTTCAAGAGAAAGCATCAGAGCTGTGAAGAAACTGGATCGACTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atatgta