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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcctgcacacaaaccatgtgaacactgcagagattagatgttcgccttgttgtgaattttgtattcatgggtgcagtgggctacacatgaattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT

Basic information

species Zea mays
transcript GRMZM2G103812_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103812_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 1
-----cgcctgcacacaaaccatgtgaacact-gcagagattagatgttcgccttgttgtga--attttgtattcatgggtgcagtgggctacacatgaattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT
      |  |        ||  | ||||||   | | || | |||  |||     | ||| |  | ||||| || |||| |    ||    | |||||||     |||| |||||||||||||||||||||||||| |  ||||||||  |||| ||||  || |||||||||||||| ||||||||||||||||| ||||||||  |
ttacatggtttattcttgacagtctgaacaaaagaataggtcagagtttcttgcaggtgtcatgaatttgttttgatggatt--atgaatca-acatgaa-----cagGTACTGGAATTAACAAGCCGGATTACCTGGGTACGGTGGACGTGGACCCCAATTCCCCTACATACTCCCAAGTGATCCACAGGCTCCCAGTCACCCATGT
















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|149083207|gb|EE172484.2|EE172484
EST:     GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACG                         GCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
genomic: GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
EST: gi|211184169|gb|FL127370.1|FL127370
EST:     GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACG                         GCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
genomic: GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
EST: gi|31354133|gb|CD438490.1|CD438490
EST:     GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACG                         GCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
genomic: GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
EST: gi|29167955|gb|CB411215.1|CB411215
EST:     AAGCTCGTCTACGTCACCTGCGTCTACAACG                         GCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
genomic: AAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
EST: gi|5567017|gb|AI881928.1|AI881928
EST:     GCAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACG                         GCACTGGAATTAACAAGCCGAATTACCTTGCGACGGGGGATTTGGATCCCA
genomic: GGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
EST: gi|67031397|gb|CO460146.1|CO460146
EST:     CCCAGGGAGTAGCTCGTCTACGTCACCTGCGTCTACAACG                         GCACCGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA
genomic: CCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 368

TGCTGCCACGCCGCCAAGGGGCCCGGGTACGCCACGCCGCTGGAGGCCATGGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2209

TGCTGCCACGCCGCCAAGGGGCCCGGGTACGCCACGCCGCTGGAGGCCATGGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1285

TGCTGCCACGCCGCCAAGGGGCCCGGGTACGCCACGCCGCTGGAGGCCATGGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

TGCTGCCACGCCGCCAAGGGGCCCGGGTACGCCACGCCGCTGGAGGCCATGGAGAAGGGCCCCAGGGAGAAGCTCGTCTACGTCACCTGCGTCTACAACGgtgcgtgctt ... aattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgttgtgaattttgtattcatgggtgcagtgggctacacatgaattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT
          aattttgtattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcctgcacacaaaccatgtgaacactgcagagattagatgttcgccttgttgtgaattttgtattcatgggtgcagtgggctacacatgaattatgcagGCACTGGAATTAACAAGCCGGATTACCTTGCGACGGTGGATTTGGATCCCAGCTCTCCTACATACTCCCAGGTGATCCACAGGCTCCCGGTCACCCACAT

-gcctgca
- - - - cacaaac
- - - - - - - -catgtga
- - - - - - - - - - - - actgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctacac