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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaatttttgttccacgttttgcagctccagcagtagtctgtcttttactgacaattcatttatactttttgattggcag

Basic information

species Zea mays
transcript GRMZM2G177970_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177970_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g54020.1 (Oryza sativa), 5'ss of exon 8
CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaatttttgttccacgttttgcagctccagcagtagtctgtcttttactgacaattcatttatactttttgattggcag
|||||||||||||||| ||||||||||| ||||||||||| ||||| |||||||||||||||||||| || |||||||| || ||||||||| ||||||||||||| ||||| |  |      ||   |   |      |||     ||| ||  | || |||| ||| |   |||    | ||||
CTGTTGGTGAAGATCAGACACAACATTTGGAATTAACTCGCGAAATCGCTGAGCGTGTAAATAATCTATACGGTGGAAGGAAATGGAAGAAAATGGGAGGgtgaga-aaattatattattttattccacttttttgt--gtaaataatctattg-taacgattcttttttgtatttgttcttgcag

upper sequence: GRMZM2G177970_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA06G09240.2 (Glycine max), 5'ss of exon 4
CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaatttttgttccacgttttgcagctccagcagtagtctgtcttt-----tactgacaa-ttcatttatactttttg-attggcag-------------------------------------
||||||||||||||||||  || || || || || ||||||||  | ||||| || || |||||| | ||||| |||||||||||||||||||| || ||||||| ||| | |||||     |  |   |   ||| |  ||   ||   ||     || |   |  ||| ||||||  ||||| |||||                                        
CTGTTGGTGAAGATCAAAAGCAGCACTTGGAGTTGACTCGTGACTTGGCTGAACGGGTTAATAATTTATATGGAGGAAGAAAGTGGAAGAAATTAGGCGGgtgag-taattgtttgtaaactggatgtaaaaaccatccataagatggggttgaaattatttgtagcttcttttatagattttgcattgggcttgaccgttttttcttttattttgtacatttatgacag

upper sequence: GRMZM2G177970_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA04G09130.2 (Glycine max), 5'ss of exon 8
CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaatttttgttccacgttttgcagctccagcagtagtctgtcttttactgacaattcatttatactttttgattggcag
| ||||||||||||||||  || ||||| || || || |||||  | ||||| || || |||||| | ||||| |||||||||||||||||||| || ||||||| ||| | |||||     |      |   ||| |  ||   |||  ||       |||  |||||   | ||| || |    
CCGTTGGTGAAGATCAAAAGCAGCATTTGGAGTTGACCCGTGACTTGGCTGAACGGGTTAATAATTTATATGGAGGAAGAAAGTGGAAGAAATTAGGCGGgtgag-taattgtttgtaaactggacgtaaaaaccatccataagatgtggttgg-----aat--atttagcttcttttatag----

upper sequence: GRMZM2G177970_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 5'ss of exon 8
CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataa-atttttgttcc-acgttttgcagc---tccagcagtagtctgtcttttactgacaattcatttatact-ttttgattggcag-----------------------------------
| ||||| || ||||| |  || ||| | ||| | || |||||  | ||||| ||||| ||| || | ||||| ||||| |||||||||||||||||||||||||| || ||||||  ||| |   | || |     |     |  || ||   ||||  | | || |  ||||     ||||  |  |||                                    
CAGTTGGGGAGGATCAGAAGCAGCATCTGGAACTGACCCGTGAGCTGGCTGAACGTGTTAATTATTTATATGGAGGAAGGAAGTGGAAGAAATTGGGAGGgtgagaaaatatttttcctcctaaaatatgaaaagtattttctatgagactcaattttgttcaaaacttttttacctaatttttttctgcatcactgacttgattgcatcttttatttttttcacag

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|76294199|gb|DV033767.1|DV033767
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAGGTTCCTGA
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAGGTTCCTGA
EST: gi|32944158|gb|CF048977.1|CF048977
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAG
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG
EST: gi|50331394|gb|CO526520.1|CO526520
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAG
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG
EST: gi|32930432|gb|CF035244.1|CF035244
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAG
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG
EST: gi|71449703|gb|DR830753.1|DR830753
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAG
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG
EST: gi|32930572|gb|CF035384.1|CF035384
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGTAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAG
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG
EST: gi|78120428|gb|DV538812.1|DV538812
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAGGT
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAGGT
EST: gi|71449704|gb|DR830754.1|DR830754
EST:     GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGG                         GAGAGGGGGTTTGCTATTTAAG
genomic: GAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 22 (downstream exon)
Score: 28

CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG


Block sizes: 48 (upstream exon), 22 (downstream exon)
Score: 36

CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG


Block sizes: 45 (upstream exon), 22 (downstream exon)
Score: 7

CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG


Block sizes: 41 (upstream exon), 22 (downstream exon)
Score: 11

CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaa ... tgattggcagGAGAGGGGGTTTGCTATTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTTGGTGAAGATCAAACACAACATTTAGAATTAACTCGTGAAATAGCTGAGCGTGTAAATAATCTTTATGGTGGAAGAAAGTGGAAGAAATTGGGAGGgtgagataaatttttgttccacgttttgcagctccagcagtagtctgtcttttactgacaattcatttatactttttgattggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA