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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagcagtttcagataactcgcttgggctaacgacgtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag

Basic information

species Zea mays
transcript GRMZM2G152127_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 18
CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggc---------agcagtttcagataactcg-----cttgggctaacgac-gtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag
|||||||||||||||||| || |  || ||||| ||||| || ||||| || ||||| || |||||||||||||||||||||||||| ||| | || |||||| |           |  |  |||    || |       |||||  || |  | |||  | || || || ||  ||   |   | |  | |  ||||  |  ||
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttcctgcaatttaaggtacttggattatcatccgtc--taaatctggaactctgtccgacaatct--gccatttttttt-tag

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatgg--cagcagtttcagataactcgcttgggctaacgacgtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag----------
 |  || ||||| || ||| |    || || |||||||| || ||||||||||| || || |||||||||||| |||||||| |||| ||| |||||||||||        ||  |||     | |   ||   ||    |  | |   |   | |  |||   ||  ||    ||      |    ||             
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcact--tcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc

upper sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA11G02030.1 (Glycine max), 5'ss of exon 17
CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatgg--cagcagtttcagataactcgcttgggctaacgacgtcggtgaagcttgaccttcgtgtt-aatgtttttgtcgcttttcgtgcag---------
 | ||| |||||  | |||||    |  || |||||||| |||||||||||||| || || || ||||||||| |||||||| |||| ||| |||||||||||        ||  |||  |  | |   ||   ||    |  | |   |   | |  |||   ||  |||    ||      |    ||            
AAAGGCAGTTCACATTGACCCAATTCAATTTGACATGGAACGCGACCTTATCACTCCAACATATAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctcaggatttcatttcact--tcatattgaatagaataggtcttaaagtggaataacctttataaatggaatgttattttttccc

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|33096859|gb|CF056819.1|CF056819
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCGCAGCTGCTGAAACACTATCAG                         AGCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTTTGCA
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCA
EST: gi|86470254|gb|DY236624.1|DY236624
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|33770959|gb|CF273253.1|CF273253
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCGCAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTATAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|211196583|gb|FL038431.1|FL038431
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCA
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCA
EST: gi|5688735|gb|AI941750.1|AI941750
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|71426982|gb|DR808032.1|DR808032
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|60349126|gb|DN216099.1|DN216099
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|60339626|gb|DN206599.1|DN206599
EST:     CACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: CACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCT-GAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|6020548|gb|AW065476.1|AW065476
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCGCAGCTGCTGAAACACTATCAG                         ACCATCATTGACG
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACG
EST: gi|60358314|gb|DN225287.1|DN225287
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|94473569|gb|EB702527.1|EB702527
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTTTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|166478491|gb|EG287455.1|EG287455
EST:     CTGAAACACTATCAG                         ACCATCAATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTC
genomic: CTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATC-ATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTC
EST: gi|74246154|gb|DT654068.1|DT654068
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|74239652|gb|DT647566.1|DT647566
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
EST: gi|16920190|gb|BM074544.1|BM074544
EST:     TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAG                         ACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC
genomic: TCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCC

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), 48 (downstream exon)
Score: 115

CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCCACCTGTTGCCTCACGGCATGGAGAATCAAAATGCTTTGCTAGCCGTCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 56

CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCCACCTGTTGCCTCACGGCATGGAGAATCAAAATGCTTTGCTAGCCGTCAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 43

CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCCACCTGTTGCCTCACGGCATGGAGAATCAAAATGCTTTGCTAGCCGTCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 104

CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagc ... tttcgtgcagACCATCATTGACGGTATGTACAATAGCATGAAGTAGGCTCTGCACGGCTCCACCTGTTGCCTCACGGCATGGAGAATCAAAATGCTTTGCTAGCCGTCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatggcagcagtttcagataactcgcttgggctaacgacgtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT