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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaaaatgctgtgtaacaactctatgatgatcacttggatagtttttgttatttgcaccagttctttatcttttatatgagtgtgctgataccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG

Basic information

species Zea mays
transcript GRMZM2G091119_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091119_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 6
gtatgtcaaaatgctgtgtaacaactctatg--atgatcacttggatagtt-tttgttatttgcaccagttctttatcttttatatgagtgtgctgataccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG
||| || | ||   ||  | |||| | | ||  ||  ||  || |||  || |||| || |  ||  |   | || | |  ||| | |   || |  ||| ||||| |||||||||||||| || ||||||||||| || |||||||||||||| || |||||||||||||||||   ||||||||||
gtaagtgacaacattgcattacaattttctgccattttcctttagattcttatttgctactctcattataccctt-tttaatattttatactgtt--tacaacatgaagCCATCCATCACCTTCAGTGCTTATACCCGCACTACGAACTGTTGGAAATATTGTAACTGGAGATGACGCGCAAACTCAG

upper sequence: GRMZM2G091119_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 6
gtatgtcaaaatgctgtgtaacaactctatgatgatcacttggatagtttttgttatttgcaccagttctttatcttttatatgagtgtgctgataccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG
    || |  |  |||  |     ||| |  |||   |     | |  | |  |    ||   || ||   |  |   ||  | | ||| ||  |  |  || ||| || ||||| || || ||||| || |||||||| ||||||||||| || ||||| ||||||||||||  ||| ||||||
----gtgagtactctgctt-----ctcgaatatggctatgcaaaaatatatgctcccatgtgtcattttaatgccaaatac-taaatgtcctact--cttattcagGCACCCATCCCCTTCAGTGCTAATTCCTGCTCTTCGAACTGTTGGAAATATTGTCACTGGAGATGATATGCAGACTCAG

upper sequence: GRMZM2G091119_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 6
gtatgtcaaaatgctgtgtaacaactctatgatgatcacttggatagtttttgttatttgcaccagttctttatcttttata-tgagtgtgctgataccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG
    || |  |  |||  |  ||| |  |||   ||  |    |||  |  |   || | ||     | || ||     | | | | ||||||  |  |  || ||| || ||||| || || ||||| || |||||||| ||||||||||| || ||||| ||||||||||||  ||| || |||
----gtgagtactctgcttctcaaat--atggctat-gcaaaaatatatgctcccatgttca-----ttttaatgccaaacactaaatgtgctact--cttattcagGCACCCATCCCCTTCAGTGCTAATTCCTGCTCTTCGAACTGTTGGAAATATTGTCACTGGAGATGATATGCAGACACAG

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|32795378|gb|CD947614.1|CD947614
EST:     CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCT                         CCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
genomic: CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
EST: gi|211478265|gb|FL127102.1|FL127102
EST:     CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCT                         CCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
genomic: CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
EST: gi|32856329|gb|CD996010.1|CD996010
EST:     CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCT                         CCATCCATCACCGGCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
genomic: CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
EST: gi|60397633|gb|DN230449.1|DN230449
EST:     GCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCT                         CCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
genomic: GCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
EST: gi|211099873|gb|FL161944.1|FL161944
EST:     AGCTGTAATTGAAGCTGGTGTTTGCCCCCCGGCTTGTGGAGCTCCTTTCT                         C-ATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGGACA
genomic: AGCTGTAATTGAAGCTGGTGTTTGCCCCC-GGCTTGTGGAGCTCCTT-CTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACA
EST: gi|32789318|gb|CD941554.1|CD941554
EST:     CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCT                         CCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT
genomic: CAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACAT

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: 869

ATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCACTAATGATAAGATCCAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 222

ATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCACTAATGATAAGATCCAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

ATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCACTAATGATAAGATCCAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 285

ATGCTTGCTGGGCTTTGTCATACTTATCTGACGGCACTAATGATAAGATCCAAGCTGTAATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTTCTgtatgtcaaa ... ccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttatttgcaccagttctttatcttttatatgagtgtgctgataccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG
                                     tgctgat  putative branch site (score: 285)
               ttctttatcttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcaaaatgctgtgtaacaactctatgatgatcacttggatagtttttgttatttgcaccagttctttatcttttatatgagtgtgctgataccacatgcagCCATCCATCACCGTCGGTGCTTATACCTGCTCTACGAACTGTTGGGAACATTGTAACTGGAGATGATCAGCAAACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG