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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attggtataaccgaacatgcccttagtaaattgatgcatgcaataagtttggttgatatatatcatattttgtgatagtaactatattgtgtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT

Basic information

species Zea mays
transcript GRMZM2G048804_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048804_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g07100.1 (Oryza sativa), 3'ss of exon 4
--attggtataaccgaacatgccct-tagtaaattgatgcatgcaataagtttggttgatatatatcatattttgtgatagtaactatattgtgtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT
  | | | ||||    || | |  | |  | |||     ||||     |||||| ||  |   ||||| |||||||||| | |||||||| ||  ||| ||||||||||||||||||||||| || || ||||| ||| || |||||||||| |||||||||||||| |||||||| || |||||  ||||||| ||||||||
tgaattgaataag-atacttactttattatgaatgagaacatgtttctagtttgatttgttagtatcacattttgtgattgaaactatat-gta-aaccttagATCGTATCAGAAAGATGTACGACGCCTTCCCCAGGATATCTGTTCCACACTTCCTTGGAGATGATTATGATGACGACGGGCAGAAATTATCCGAAGCTAT
















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|211028765|gb|FL344477.1|FL344477
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAA
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAA
EST: gi|33771157|gb|CF272818.1|CF272818
EST:     AGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: AGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|71773197|gb|DR971110.1|DR971110
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|94472951|gb|EB701909.1|EB701909
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAAAAAGATGTATGAGGCATTCCCAAAGGG-AACTGTTCCACAT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAA-GGGTAACTGTTCCACAT
EST: gi|33467112|gb|CF244161.1|CF244161
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|211412124|gb|FL339002.1|FL339002
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|31558704|gb|CD527916.1|CD527916
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|50339822|gb|CO534948.1|CO534948
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|31349428|gb|CD433785.1|CD433785
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|32850448|gb|CD990129.1|CD990129
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
EST: gi|74236761|gb|DT644675.1|DT644675
EST:     TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTG                         ATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT
genomic: TGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATT

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: 43 (upstream exon), 48 (downstream exon)
Score: 55

GTTACCTGTGGTGGTGAACTTGCTGTCCTCTTTGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 59

GTTACCTGTGGTGGTGAACTTGCTGTCCTCTTTGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 58

GTTACCTGTGGTGGTGAACTTGCTGTCCTCTTTGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

GTTACCTGTGGTGGTGAACTTGCTGTCCTCTTTGTTGACACCCTCATCACAGGAGAGCTTCCATATAGTGAACAAATTTTTGgtcagttttt ... gtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttggttgatatatatcatattttgtgatagtaactatattgtgtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT
          atatatatcatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attggtataaccgaacatgcccttagtaaattgatgcatgcaataagtttggttgatatatatcatattttgtgatagtaactatattgtgtaacattagATCGTATCAGAAAGATGTATGAGGCATTCCCAAGGGTAACTGTTCCACATTTCCTTGGAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - -catgccc
- - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - ttggttg