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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG

Basic information

species Zea mays
transcript GRMZM2G126913_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126913_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 4
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagta---------gacaagtagatggaaccgtttgt-----tattt-----ttcttatgcttgatttgccaatgaatc--cagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
||||||   || |    ||||||| |||   | ||   ||| | |   |          |||   | |||  | | ||| |     || ||     ||||||   ||||||  || ||   |   |||||||||||||||||||||||| || ||||||||||| || ||||||||||| ||||||||||||||||||||||| || ||||||||||| |||||||||
gtttgtgaaacatat-gcatattttgtgaact-attgcagtaacatacatcattgtgtaacataaatatgccatcttttatatggataattgttggttcttacaattgattaaccgatttttttgcagTGGTGGCTACAACATTAAGACTGGACCAGGCTGCAGTATTGAGCTGATGAAGTTTGACATGGGAGGCTCTGCAGCAGTTTTTGGTGCAGCAAAAGCTTTG

upper sequence: GRMZM2G126913_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaaccg-tttgttatttttcttatgcttgatttg-----ccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
           |  | |   |||  ||     | | ||  |||       || ||  | |        |||||||||||  |  |  ||||||||     |   || |  |||||||||||||||||||||||| || || ||||||   || ||||| |||||||| |||||||| || || || |||||  |||| || || |||||| | 
----------gtaactaatcattctgtattgctttgaattttactctgttacgagctggtatcttttctttgttattttagtggttgttgatttgaatatcttgtgtacacagTGGTGGCTACAACATTAAGACTGGACCTGGCTGCTCAATTGAGCTCATGAAATTCGACATGGGCGGTTCAGCTGCTGTTCTTGGCGCTGCGAAAGCTATT

upper sequence: GRMZM2G126913_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaacc-gtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
             |    | |  | || || || |    |    |   |      ||  |   ||   || ||||||   |  ||| ||  ||||   |      ||| ||||||||||||||||| |||||||| ||||||   || ||||| |||||||| || |||||||| || || |||||  |||| || || |||||  | 
-------------gtactagagct-gttggcttctgtttgccgcatcaatctctttatttaatacttattagttattgaccagatggtt--tttgttca------cagCGGTGGCTACAACATTAAAACCGGGCCTGGCTGCTTAATTGAGCTCATGAAATTCGATATGGGAGGTTCAGCTGCTGTTCTTGGCGCTGCAAAAGCCATT

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: 46 (upstream exon), 49 (downstream exon)
Score: 341

CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACATCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 715

CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACATCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 435

CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACATCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 441

CTGCTAACCCTCCTCACTTCATCCATTTGTGCTACAAACCCACTGATGGGAACATCAAGAGAAAGCTGGCTATTGTTGGGAAGGGTTTAACTTTTGACAGgtttgtagta ... atgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtagatggaaccgtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG
                                gcttgat  putative branch site (score: 441)
               tttgttatttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtagtacttgccacatatttagtgggtttataaaagttagaagtagacaagtagatggaaccgtttgttatttttcttatgcttgatttgccaatgaatccagTGGTGGCTACAACATTAAGACCGGGCCAGGCTGCAGCATCGAGCTGATGAAATTTGACATGGGAGGCTCTGCAGCTGTATTTGGTGCAGCTAAAGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT