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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttgtggaatcttcttttctaatgtcacctccattttctttttctttgacatgttatttgtctttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG

Basic information

species Zea mays
transcript GRMZM2G083076_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 4
gtaacatttgtggaatcttcttttcta------------atgtca----cctccattttctttttctttgacatgttatttgtctttat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG
|||  | || ||  |  | ||||| ||            ||| |     ||  | |||||||| |  |  || |  | ||  | || || ||  || |||||||| ||||| |||||||| |||||||||||||| |||||||  ||||||||||| |||||||||||||| ||||| ||||||||||||||||||
gtatgactt-tgctacttgcttttatatgacaagaacaaatgccctattccatcgttttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

upper sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 4
gtaacatttgtggaatcttcttttct-----------aatgtcacctccattttctttt-----tctttgacatgttatttgtctttat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG
|||  | || ||  |  | |||||||           ||||||    || ||||| |||     |  |   |    | ||  | || || ||  || ||| | || ||||| |||||||| |||||||||||||| || ||||  ||||||||||| |||||||||||||| ||||| ||||||||||||||||||
gtacaactt-tgctacttgcttttctatgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

upper sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 4
--------------------gtaacatttgtggaatcttcttttcta-atgtcacctccattttctttt-tctttgacatgttatttgtctttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG
                     |  ||||  ||  | || ||    |  || | |   |  |||| |||| | |   ||    |  ||    ||  || ||||||||| || |||||| |||||||||| || ||||| ||||| ||||  || |||||||| ||     |||||||| ||||||| ||||||||||| || 
gtgtatatacattaattagattgtcattgttgtcacctactgggatgtatttaataacttttttgttttatttccaactcactgatttctgttgcttgcagTCGGCCTTCGGAAGATCGAACTATTCCCTTGAGTGTAATTGCAGAGCGTACAAAGCTTTCTATAGAGAATGTGGAGCATCTCCTCATGAAGAGCCTATCT

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|32944901|gb|CF049720.1|CF049720
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|60342361|gb|DN209334.1|DN209334
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|78180907|gb|DV551280.1|DV551280
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|211163793|gb|FL451880.1|FL451880
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|149111477|gb|EE294981.2|EE294981
EST:     AAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|148943272|gb|EC888334.2|EC888334
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAT                         TCGGCCATCTGAAGATAGAACTTTTCCATTAAGTGTTATTGTTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|78103809|gb|DV522237.1|DV522237
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|60672250|gb|DN475016.1|DN475016
EST:     AAGCTGCTTGAGAGAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGGAGATAGGACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|110942146|gb|EE162303.1|EE162303
EST:     AAGCTGCTGGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|12047287|gb|BF729426.1|BF729426
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|8401231|gb|BE056865.1|BE056865
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|71325796|gb|DR799577.1|DR799577
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|211050666|gb|FL481059.1|FL481059
EST:     AATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAMCTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
EST: gi|116829258|gb|EC866181.1|EC866181
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacatttg ... ttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatgtcacctccattttctttttctttgacatgttatttgtctttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG
                                      tttgtctttattttc  CT-rich tract
                                   ttatttgtctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatttgtggaatcttcttttctaatgtcacctccattttctttttctttgacatgttatttgtctttattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA