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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaacctctccaatatcgacatccaaacggagcataattcttctataccctttttgttgaaaattttacttgtgttgatttcaacttcaaaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT

Basic information

species Zea mays
transcript GRMZM2G028089_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 8
tccaacctctccaatatcgacatccaaacggagcataattcttctataccctttttgt-tgaaaattttacttgtgttgatttcaacttcaaaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT
    | ||  | |     ||     |   | | ||||||  || | ||| | ||| |  |   |    |    ||||   |   |   |   ||  || ||||||||||||||| ||||||||||  | ||| | |  || |||||  ||||| |||||||||||||||||||||||||||||||| |   |  || |   
agttatctgccaagagatgaagagaagttgaatcataatggttgtttactcgtttggcattgcacccatgtcagtgt-attaatactcttgtaacttgcagCACAATGAATGAGCTGGTCGAGAAGTTTAACGCGACATACGAGAGGTCGACTGCCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGATTTTCCCCCTTCTG
















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|211278074|gb|FL458563.1|FL458563
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|5343228|gb|AI795413.1|AI795413
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|37383993|gb|CF629039.1|CF629039
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|37378561|gb|CF625975.1|CF625975
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|71428766|gb|DR809816.1|DR809816
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|78079913|gb|DV508325.1|DV508325
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|5847033|gb|AW000112.1|AW000112
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CCCAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|78104235|gb|DV522653.1|DV522653
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|74245515|gb|DT653429.1|DT653429
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
EST: gi|37387432|gb|CF630909.1|CF630909
EST:     AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAG                         CACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC
genomic: AACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGAC

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: 125

GAATACAACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

GAATACAACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 50

GAATACAACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 51

GAATACAACGACACTCTCCTCATGACTTACCTGGCAATGTTCACTAACTGTTCAAGgtatgcactc ... aaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccctttttgttgaaaattttacttgtgttgatttcaacttcaaaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT
                            tgttgat  putative branch site (score: 51)
      tttttgttgaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaacctctccaatatcgacatccaaacggagcataattcttctataccctttttgttgaaaattttacttgtgttgatttcaacttcaaaatctgtagCACAATGAATGAGTTGGTCGAGAAAATCAACACAAGCTATGAGAGACCGACTACCAGGAGAGGAGGCCGAGGTGCTTTCATGTAGCTCACCTGCCATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
-ccaacct
- - - - - - - - - - catccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat