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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA

Basic information

species Zea mays
transcript GRMZM2G402242_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 6
gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacg-tgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA---------------------------
                |    ||||| |       |||  |  || |  |||||| ||  |  |  | | | || |  || |    |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| |||||                           
----------------gttagtgctgatc-----attcctttgtcctttttttgggtggttgatgttaatgctgattttctttatatatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATCCCAAGATGCAAGCCTTTCAAATACACCTACGAGAAGGAGATTGTTAT

upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 5
gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA----------------------
             ||  |   || |  ||||   || |  | ||      | |||||||  | ||| | |   ||     |  || |||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||                      
-------------gttagtgctgatcattcctttgtccttttttt---tctgtggttga--tgttaaggctgattttctttatat-atagGTTAAGTAGATGTACCTTTATAACTACTGGCGAAGATGGGCCAATCCCAAGATGCAAGCCTTTCAAATACACCTATGAGAAGGAGATT

upper sequence: GRMZM2G402242_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g00440.t01 (Vitis vinifera), 3'ss of exon 5
gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatact--tttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA----------------------------------
   ||      |  |||| ||  || | |      |||||  ||| |     |||  ||      |  |||  || |||   | | || |||  | ||||| || || | |||||  |||||||||||||| ||||| |||||||||||||| || ||                                  
--gtaatgcattgataggttaaactttctttttctttcaggcttcttctcgcttttctttctggctgctgagttgatgcatttactttgtagACTGAGTAGGTGCACTTCTATAATCACTGGTGAAGATGGACCAATTCCAAGATGCAAGCCTTTTAAGTATACCTATGAAAAGGAGATTGTTATATATCCT

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|91872707|gb|EB402664.1|EB402664
EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAG
EST: gi|87157289|gb|DY402078.1|DY402078
EST:     GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAG                         GTTAAGTAGATGTACCTTTATAACTACTGGTG
genomic: GACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTGGTGATATTGCAAGgtatatgttg ... tgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA
                  ggttgac  putative branch site (score: 4)
                                      ttgctcct  putative PPT
                       actttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgttgcttgtaggatatgctgtttccagagttcagtgttcatacttttggttgactttttatgacgtgttgctcctgcattatagGTTAAGTAGATGTACCTTTATAACTACTGGTGAAGATGGGCCAATACCAAGATGCAAGCCCTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG