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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagataatctttcaatctgaacctttagttccaactgctcttgatggtggcgctgagactttgtgttgcatatattgcttgcttaaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG

Basic information

species Zea mays
transcript GRMZM2G168143_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 7
gtatgcagataatctttcaatctgaacctttagttccaactgctcttgatggtggcgctgagactttgtgttgcatatattgcttgct-taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAAC-CGCTGAATTTTGCAGCTGACATTTTGTGTTG
    | | |||  |||   | |   ||||||         |  | |        | |       ||||  |   | || |||| || | |   ||| |||||||||||||   || ||||||||||| ||||||| ||| || |||||||| ||||| |||||||||  |    |||||| |      |  ||| | || 
----gtatatatgcttctgaaccttacctttttgcatggataatttaagaatctgagtaattcttttgcatgctaaattttgcatggtatcgttgttagGAATCGACTGGGCTGATTACAAGAAGCAACTGAAGAAGGGCGAGCAATGGAACGTGGAAGTCTACTAATTCTTCCAATTTTCCTCACATCTGTTTCTTTT-

upper sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G20020.3 (Arabidopsis thaliana), 3'ss of exon 8
gtatgcagataatctttcaatctgaacctttagttccaactgctcttgatggtggcgctgagactttgtgttgcatatattgcttgcttaaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG------
   |    | |     | |||   |  ||  | |||      |  |   ||     ||    ||  | |  ||  | | | |          | | ||| || |||||||| || |||||||||||| |||||| || ||| |||||||| || || ||||||| | |    |   ||     ||||||||  ||| |      
--gtaagaagagctaattaat--aacactccaattcttgaaacattcattgcataagcaataacactctaatgactttgtggt-------ggttttagGTATTGACTGGTTTGATTACAAGAAGCAGTTGAAGAAGGCAGAGCAATGGAACGTTGAAGTCTACTGATCAAAAAGCCTT-----TGACATTTC-TGTAGCAAAGT
















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|32942069|gb|CF046888.1|CF046888
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|134768979|gb|DY742724.1|DY742724
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|32845747|gb|CD985428.1|CD985428
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|71441571|gb|DR822621.1|DR822621
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|32844901|gb|CD984582.1|CD984582
EST:     CATGGAGAAGGGTATCGATGCCATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTCCAAGAACCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|32844778|gb|CD984459.1|CD984459
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|32834515|gb|CD974193.1|CD974193
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|89246872|gb|DY618658.1|DY618658
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|8665549|gb|BE186365.1|BE186365
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|76923045|gb|DV169307.1|DV169307
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTCCAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
EST: gi|78122840|gb|DV541224.1|DV541224
EST:     CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACG                         GAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA
genomic: CATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 32

GAGCTCCTGAAGAAGGACAACACCTACGTCTACATGTGTGGGTTGAAAGGCATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 198

GAGCTCCTGAAGAAGGACAACACCTACGTCTACATGTGTGGGTTGAAAGGCATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 28

GAGCTCCTGAAGAAGGACAACACCTACGTCTACATGTGTGGGTTGAAAGGCATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GAGCTCCTGAAGAAGGACAACACCTACGTCTACATGTGTGGGTTGAAAGGCATGGAGAAGGGTATCGATGACATTATGGTGTCACTGGCTGAAAAAGACGgtatgcagat ... taaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgatggtggcgctgagactttgtgttgcatatattgcttgcttaaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG
 tcttgat  putative branch site (score: 155)
                                       cttgctt  putative PPT
                               atatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagataatctttcaatctgaacctttagttccaactgctcttgatggtggcgctgagactttgtgttgcatatattgcttgcttaaatgtcagGAATCGACTGGTTCGACTACAAGAAGCAGCTGAAGAGGGGAGATCAATGGAATGTGGAGGTCTACTAACCGCTGAATTTTGCAGCTGACATTTTGTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA