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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attactgttaataaggtttgctgcagttgttactataactagggcatatagcttcggtgtcctcctatgtttatcagaagtcgatcatttttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG

Basic information

species Zea mays
transcript GRMZM2G124883_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 18
----atta--ctgttaataaggtttgctgcagttgttactataactagggcatatagct-tcggtgtcctcctatgtttatcagaagtcgatcatttttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG
     |||   ||||||||   |||  | |||| | | ||      |   | | | | | |   | |  ||||   |  ||   |     ||  | ||  |||||||||| ||||| ||||||| |||||| |||| ||||||||||||||||| || || | |      ||| ||||||||||   ||||   | ||| |||||||
acttgttaacttgttaatatacttttgt-cagtagcttctccgttca---cctttggttattaatattatcctgcctcgatttca---taattgtgttattgtccagGTTGCATCTTTGAAAGATACAATAGCACGAAAAGATATGGAAATCGAACAGCTTCAGCTCCTTAAATCCAAATCTCCCAATTCAATGACAGACAGAAATG
















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|76018055|gb|DT945225.1|DT945225
EST:     AAGATATAAAAGAGCTGCTAGAACAG                         GTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
genomic: AAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
EST: gi|211077350|gb|FK960594.1|FK960594
EST:     CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAG                         GTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
genomic: CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
EST: gi|211077349|gb|FK960593.1|FK960593
EST:     CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAG                         GTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
genomic: CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
EST: gi|211077348|gb|FK960592.1|FK960592
EST:     CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAG                         GTTTCATCTCTGAAAGACACAATATC
genomic: CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATC
EST: gi|211077347|gb|FK960591.1|FK960591
EST:     CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAG                         GTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA
genomic: CTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 166

AATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 40

AATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 15

AATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 102

AATAAGCACTTTGAAGTTTGCTGAAAGGGTTTCTGGAGTTGAGTTAGGTGCTGCAAGAAGTAACAAAGAGGGTAAAGATATAAAAGAGCTGCTAGAACAGgttcttacaa ... ttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatagcttcggtgtcctcctatgtttatcagaagtcgatcatttttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG
                                       tcattttt  CT-rich tract
                    tatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attactgttaataaggtttgctgcagttgttactataactagggcatatagcttcggtgtcctcctatgtttatcagaagtcgatcatttttgtgtccagGTTTCATCTCTGAAAGACACAATATCACGGAAAGATATGGAAATCGATCAACTCCTGAAGAACAAAGCCAAATCTCCAGGTTCATCAATAGATAGAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - -gctgcag
- - - - - - - - - - - - - -tgttact