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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttaagagtttatcatgtcctcaataattctatttattgccacattttctctatattttttagagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g54640.2 (Oryza sativa), 3'ss of exon 8
gtgctttaagagtttatcatgtcctcaat--aattctatttattgccacattttctctatatttttta-gagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA
||| || | || || ||||| ||||   |  | || ||| | || | |  | |||||   || ||| | || || | |||  ||| |  | |   ||| | ||||| ||||| ||||||||| | |||||||||| | ||| ||| |||||||||||||||||||| |||||||||    
gtgattcacgaattcatcatctcctttttttagttttatat-ttccaaggtgttctcgggatatttcatgataaatgcat--gaacacatgcatatttctgtgcttttagAGATTCATAAACCGGACTAAGCCGCCATTAACCAAGGATCAGCAACAAAACCTTACAAGATGGGCA----

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G14970.1 (Glycine max), 3'ss of exon 8
gtgctttaagagtttatcatgtcctcaataattctatttattgccacattttctctatattttttagagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA
     |||||  | |   || |  |    |  | |   ||||     | |  | ||||  | | || | |||   |   |||  | ||    ||||||  | || |||| || || |||||||| ||||| |  || |||||||||||||||||||| || || |||||||||    
----gttaagtatct-ctatttttttgtaagatgtggatattatactact--cactattatatcta-ataataatactagaaagaattgttttttgtt--cctgcagAGATTTATTAACAGAACCAAGCCACCCCTCAGCAAAGATCAGCAACAAAATCTCACAAGATGGGCA----

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 8
gtgctttaagagtttatcatgtcctcaataattctatttattgccacattttctctatattttttagagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA
     |||||  | |   || |  |    |  | |   ||||   | | |      |  | | | | | |||   |   |||   |||        ||| | || |||| || || |||||||| ||||| | ||| |||||||||||||||||||| || || ||||||||     
----gttaagtatct-ctatttttttgtaagatgtggatatt---atactactcgcaattatctcaaataataatactagaaagttttt-------tttccctgcagAGATTTATTAACAGAACCAAGCCACCACTCAGCAAAGATCAGCAACAAAATCTCACAAGATGGGCC----

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 8
gtgctttaagagtttatcatgtcctcaataattctatttattgccacattttctctatattttttagagaattcca-tctgaagaatttcccgtttgtttgcttgt-agAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA
           |||| |  |  | || ||     |   |||  | |   ||||   | ||        ||  |  | ||| ||     | |      | | ||  | |||| || |||||| | |  ||||| || || |||||||||||||||||||| ||||||||||||||     
-----------gtttgttctaacttccat----ttccctatcacgaagctttccacaaatccaactttgatctataatctcaactccctgcttcccatgttctcttcagAGATTTATAAACCGTAGCAAGCCACAGCTCAGCAAAGATCAGCAACAAAATCTTACCAGATGGGCT----

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|149100297|gb|EE186362.2|EE186362
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG                         AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG                         AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAT
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCAACCTTCAG                         AAGTTCATAAACAGAAC
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAAC
EST: gi|91872112|gb|EB402069.1|EB402069
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCTCCCTTCAG                         AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG                         AAGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
EST: gi|71317337|gb|DR795362.1|DR795362
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG                         AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG                         AAGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAAC
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAG                         AAGGT-CATAAACAGAACTAAGCCCGCA-CTAAGCAAAGATCAGCAACAAA
genomic: TAGAATATGACAAAGTTGTAGGTCAATCAGCAGATCTTTTCACCCTTCAGgtgctttaag ... ttgcttgtagA-GGTTCATAAACAGAACTAAGCC-GCAACTAAGCAAAGATCAGCAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatattttttagagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA
                                 tttcccgtttgttt  CT-rich tract
     tattttttagagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttaagagtttatcatgtcctcaataattctatttattgccacattttctctatattttttagagaattccatctgaagaatttcccgtttgtttgcttgtagAGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG