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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagctctcttcacagcttaggagatttttactcatgatttcagctgaagttttaacaagtgctttgagtattctgaaacttgtcgctctatattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA

Basic information

species Zea mays
transcript GRMZM2G060842_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060842_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g20640.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------gtaagcaagctctct-tcacagcttaggagatttttactcatgatttcagctgaagtttta--acaagtgct-----ttgagtattctgaaacttgtcgctctatattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA
                                                |||       ||  | | |   |   || | |  |  ||||  |     | | || || ||   ||| |        |  |  ||  |  |||  ||| |  ||| ||||  ||||||||||||||||||||||| ||||  ||  | |||||  | |||||| ||||| |||||||| ||||| | |||||||||||||| | 
gtaagctcaatttgcttcctattgaacttaagaactcagaagtttgtggtaccttgtttcaatataatgtcgctggggctactctctcaacagactgggttaacttctattgcaactatcaacgataaaaaataatctaaccagtcacattatgttgaacagTTGCTTGTATCTTCAACTTCTCTATCGGCACACAGATAATTTGTCAAAGAAAGATGTTCCAGAAATTTTTATGAAGAAGAAAGTGAAAAG

upper sequence: GRMZM2G060842_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G18700.1 (Glycine max), 3'ss of exon 6
----------------gtaagcaagctctcttcacagcttaggagatttttactcatgatttcagctgaagttttaacaagtgctt-----tgagtattctgaaacttgtc----gctctatattgagt--agTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA
                 |||        | ||||    |   |   |||||     |||    |    ||   ||||   || |||     ||   ||| | | ||||  |         || || | |  ||||||||||| ||||||||  ||||||||||||| || |||||||| |  |||||| ||||  || | ||    || |||||   ||||||
gtaagacagttagagcctaaattgatattgttcatcatt---gttttttttgtgtgtgagagaaaagaaaagattaaactgttcttaccattgctcattattatacttaactgatatatcattttcaatgcagTTGCTTGTACCTTCAACTCTTGTATCAACATGCAGACAACCTATCCAGTGAAGATGTTCCTCAAATATTCAAGAAAAAGAAGTCGAAGAA

upper sequence: GRMZM2G060842_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G09720.1 (Glycine max), 3'ss of exon 6
-gtaagcaagctctcttcacagcttaggagatttttactcatgatttcagctgaagttttaacaagtgctt-tgagtattctgaaacttgtcgctctatattga-gtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA
  | | ||   | ||||    | ||||   |     |   |    |  |||||   || | || | ||||| | | ||| || || || ||   ||  | |  | | ||||||||||| ||||||||  ||||||||||||| || |||||||| |  |||||| ||||  || | ||    || |||||    |||||
gttcatcattgtttctttgtgggttagagaa-----aagaaaagatgtagctg---ttcttacgattgcttattattatacttaa-ctggtatatcattttcaatgcagTTGCTTGTACCTTCAACTCTTGTATCAACATGCAGACAACCTATCCAGTGAAGATGTTCCTCAAATATTCAAGAAAAAGAAGTCAAAGAA

upper sequence: GRMZM2G060842_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G09720.2 (Glycine max), 3'ss of exon 6
-gtaagcaagctctcttcacagcttaggagatttttactcatgatttcagctgaagttttaacaagtgctt-tgagtattctgaaacttgtcgctctatattga-gtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA----------
  | | ||   | ||||    | ||||   |     |   |    |  |||||   || | || | ||||| | | ||| || || || ||   ||  | |  | | ||||||||||| ||||||||  ||||||||||||| || |||||||| |  |||||| ||||  || | ||    || |||||    |||||          
gttcatcattgtttctttgtgggttagagaa-----aagaaaagatgtagctg---ttcttacgattgcttattattatacttaa-ctggtatatcattttcaatgcagTTGCTTGTACCTTCAACTCTTGTATCAACATGCAGACAACCTATCCAGTGAAGATGTTCCTCAAATATTCAAGAAAAAGAAGTCAAAGAAGTACAAATGA

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|76280845|gb|DV020413.1|DV020413
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
EST: gi|50327397|gb|CO522523.1|CO522523
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
EST: gi|76280844|gb|DV020412.1|DV020412
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
EST: gi|91875732|gb|EB405689.1|EB405689
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCCACTTCTGTATCAACATGCTGATAACCTATCAA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAA
EST: gi|76912690|gb|DV164849.1|DV164849
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
EST: gi|101386086|gb|EB815086.1|EB815086
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
EST: gi|50323043|gb|CO518169.1|CO518169
EST:     ACTGCTGTCAGTTATGCTTTGGGGGCTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
EST: gi|50326968|gb|CO522094.1|CO522094
EST:     ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAG                         TTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA
genomic: ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGA

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: 24 (upstream exon), 43 (downstream exon)
Score: 14

ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 67

ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 30

ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 23

ACTGCTGTCAGTTATGCTTTGGGGGTTGGTTTCAGgtaagcaagc ... tattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttttaacaagtgctttgagtattctgaaacttgtcgctctatattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA
    ttttaac  putative branch site (score: 23)
     tttaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaagctctcttcacagcttaggagatttttactcatgatttcagctgaagttttaacaagtgctttgagtattctgaaacttgtcgctctatattgagtagTTGCTTGTATCTTCAACTTCTGTATCAACATGCTGATAACCTATCAAAGGAAGATATTCCAGAAGTTTTTCTAAAGAAGAAAGTGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA