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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgacacctgacttcctgaatttttgagtctttttgttttttgtcaggtggttttgactccaatagtggtctaacatgcatcatttttccttctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC

Basic information

species Zea mays
transcript GRMZM2G054811_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054811_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g57066.1 (Oryza sativa), 3'ss of exon 6
tgacacctgacttcctgaatttttgagtctttttgttttttgtcaggtggttttgactccaatagtggt--ctaac--atgcatcat-ttttccttctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC
    | |||| ||  | | |  |  | ||   |||  || | |    ||    |||  |||| ||| |   || ||  ||||||  |   |||  ||| | ||||||| |||||||  | ||| ||||||||||||| |||||||||||||| |||||||| ||||||||||||||||||||| ||||||||||||||||| || 
-ttgaactgaattaattactactgtattccacttgaattgtct----tgtcgatgatcccaaaagttgctgctgacacatgcattttgccttctctcttttgcagACATTATTTATTATCTCCTTGTGCAACAATCAACTCTTGTATCTTATGGAAAAGGAATTAATCTGGATATTTGGTCACATTCCTGGGTTTTCTGCCTCCT
















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|67025003|gb|CO453752.1|CO453752
EST:     CTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAG                         ACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
genomic: CTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
EST: gi|5928745|gb|AW055962.1|AW055962
EST:     TCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAG                         ACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
genomic: TCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
EST: gi|6020347|gb|AW065275.1|AW065275
EST:     ATCAAGACTCATATTCAG                         ACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
genomic: ATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
EST: gi|76010546|gb|DT937716.1|DT937716
EST:     TCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAG                         ACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
genomic: TCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
EST: gi|32941084|gb|CF045903.1|CF045903
EST:     CCATCATCAAGACTCATATTCAG                         ACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA
genomic: CCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

TGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 7

TGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 9

TGACCTTGCTGGTATTATGTGTGGGCAATTTGGTGTGCCTTTCTGGGAGTTCTTGTTTGCTACTTTGATTGGGAAAGCCATCATCAAGACTCATATTCAGgtgatgtatc ... tctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggttttgactccaatagtggtctaacatgcatcatttttccttctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC
                      gtctaac  putative branch site (score: 9)
                                  tcatttttccttctat  putative PPT
                                 atcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgacacctgacttcctgaatttttgagtctttttgttttttgtcaggtggttttgactccaatagtggtctaacatgcatcatttttccttctatcgcagACACTATTTATCGTGTCCCTGTGCAACAATCAGCTCTTGTATCTTATTGAAAAGGAGTTAATCTGGATATTTGGTCACGTTCCTGGGTTTTCTGCCACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- -cacctga
- - - - - cttcctg
- - - - - - - - - - - - - - - - -tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgca