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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctttgtggaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG

Basic information

species Zea mays
transcript GRMZM5G868757_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 4
--------------gtaacctttgtg------gaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG
| | ||| | ||| | | || ||| | || | | || || | | | ||||| || || |||||||| ||||| |||||||| |||||||||||||| |||||||| ||||||||||| |||||||| ||||||| ||||||||||||||||||||||
gtatgactttgctacttgcttttatatgacaagaacaaatgccctattccatcgtt-ttctttcttctaaaccttgtgttctttttcatattgtagCCGGCCATCAGAAGACAGAACTATCCCATTAAGTGTTATAGCTGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

upper sequence: GRMZM5G868757_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 4
----------gtaacct--ttgtggaatctttttctaatgccacctccattttctttt------tctga-catgttacttgccttcat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG
| || | || | | | | |||| | || ||||| ||| ||| | | | | ||||| || || ||| | || ||||| |||||||| |||||||||||||| || ||||| ||||||||||| |||||||| ||||||| ||||||||||||||||||||||
gtacaactttgctacttgcttttctatgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
















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|194716906|gb|FK934065.1|FK934065
EST:     AAGCTGCTGGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|4804325|gb|AI666191.1|AI666191
EST:     CTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: CTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|6020410|gb|AW065338.1|AW065338
EST:     AGCTGCTTGAGAAAATCAATATTCTTTGTCTGGA-GGAGATAATCTTTAG                         TCGGCCATCTGAAAATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AGCTGCTTGAGAAAATCAATATTCTTTGTCTG-ATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|6020572|gb|AW065605.1|AW065605
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAAATAGAACTATTCCATTAA
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAA
EST: gi|60336794|gb|DN203767.1|DN203767
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
EST: gi|211013700|gb|FL252294.1|FL252294
EST:     AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAG                         TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC
genomic: AAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGAC

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), 49 (downstream exon)
Score: 227

TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 230

TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 204

TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 144

TTCACAATGCTGCTCTTACTGCACAACCAGCTTTGGTGCAGAATGAGCGGAAGCTGCTTGAGAAAATCAATATTCTTTGTCTGATGGAGATAATCTTTAGgtaacctttg ... tcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaatgccacctccattttctttttctgacatgttacttgccttcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG
                         ttctgac  putative branch site (score: 144)
 cttgccttcattttc  putative PPT
 attttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctttgtggaatctttttctaatgccacctccattttctttttctgacatgttacttgccttcattttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA