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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatataccatataacctgactcaaaagacttgcgactaactctactagagatgtattgtactaagtagaccaccggttccttccttgcag

Basic information

species Zea mays
transcript GRMZM2G177631_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177631_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 11
CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatataccatataacctgactcaaaagacttgcgactaactctactagagatgtat-tgtactaagtagaccaccggttccttccttgcag
 || || ||||||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| || |||||||||||||| |||||||| || |||||    |  | |    |||||| |  | | |||   |  ||| || | |  ||| ||   | |     ||| | ||    |||     ||||||
TGGTGGAACCCTGAAGAGTGCAAGTCCAGCTTCTCTACTGAAGGAAGCTATACATGTTATTAGCTGTGGTTACGAAGACAAGACAGACTGGGGGAAGGAGgtaagaaaccta---gacctgatt--ataaactgatggttaa-tcaattgaagacgttcctctcacctgtaaatcatgtattc-----ttgcag

upper sequence: GRMZM2G177631_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 5'ss of exon 12
CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatataccatataacctgactcaaaagacttgcgactaactctactagagatgtattgtactaagtag--accaccggttccttccttgcag---------
 || || || ||||| |  || ||||| || |||||  | ||||||||||| ||||| || ||||| || || ||||| || || |||||||||||||||||   |||   ||||  | ||  |       |    |||      |  | | |||    | |  | | ||   |  || |||   ||   |  ||         
TGGTGGAACACTGAAAATTGCGAGTCCTGCATCTCTATTAAAGGAAGCTATCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgtaactatgg-atatggcttgttttg---cccccaagacatttcattttggggattctatttggttattatttagtactggtaaattttattaagaaagaaaga
















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|32834499|gb|CD974177.1|CD974177
EST:     TACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAG                         ATTGGCTGGATTTATGGATCGATCACAGAGGATATCTTGACTGGATTTAAG
genomic: TACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatatac ... ttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAG
EST: gi|76285795|gb|DV025363.1|DV025363
EST:     GTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAG                         ATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAG
genomic: GTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatatac ... ttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAG

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: 157

CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatatac ... ttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAGATGCACTGCCATGGCTGGCGGTCTATTTACTGCATCCCGAAGCGGCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 291

CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatatac ... ttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAGATGCACTGCCATGGCTGGCGGTCTATTTACTGCATCCCGAAGCGGCCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 303

CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatatac ... ttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAGATGCACTGCCATGGCTGGCGGTCTATTTACTGCATCCCGAAGCGGCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 345

CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatatac ... ttccttgcagATTGGCTGGATTTACGGATCGATCACAGAGGATATCTTGACTGGATTTAAGATGCACTGCCATGGCTGGCGGTCTATTTACTGCATCCCGAAGCGGCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAGGGACCCTGAAGAGCGCAAGTCCAGCTTCTCTTCTGAAGGAAGCTATACATGTTATCAGCTGCGGCTACGAAGACAAGACCGACTGGGGAAAAGAGgtctatataccatataacctgactcaaaagacttgcgactaactctactagagatgtattgtactaagtagaccaccggttccttccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA