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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatatttattttatttaatagtttcaagaaatcacttcagattgctgttacagtaatcccctgatatatcgatccaactcgaactattctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA

Basic information

species Zea mays
transcript GRMZM5G892742_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g25210.1 (Oryza sativa), 3'ss of exon 6
tgtatatttattttatttaatagtttcaagaaatcacttca-gattgctgttacagtaatcccctgatatatcgatccaactcgaa-ctattctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA
  | |||   ||||||| | |  |||  |||||  |||| | | ||  | || || ||||  | | ||   | |||| |||| |||  | | ||||||| |||||||| |||||||| |||||||| || ||| |||| || |||||||| || ||||| ||||| |||||||||||| | ||  | |||||||||||||||
-ttttatgctttttattca-tgttttggagaaaatactttacgttttttttttcaataattacgtaatgcgttgatctaacttgaaattttcctgtttctagGAAGACACTGTCAGCAAGAAAAGTGAGCGCAACTAGGGGAGCTGCCTCTGTGCCTGACGAAGTATTCCACAGAGCCCAGGGGATTCAGCTATGCAACATA

upper sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0007g01660.t01 (Vitis vinifera), 3'ss of exon 6
-tgtatatttattttatttaatagtttcaagaaatcacttcagattgctgt-tacagtaatcccctgatatatcgatccaactcgaa---ctattctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA
 |  | |||| |||| |  ||       ||   |    |  | ||  || | |  |  || ||  |   || |      |  | |||     ||| | ||| ||||||||| || ||| | |||||||| |||||| |||| ||||| || ||||| ||||| || |||||||||||||||||||| || ||| | ||||| |  
gtaaaaatttgttttctcaaa-----ataaagcacatatgtatatatctatctgtaaaaagccatttgaatgttagatgacatagaaaagtgattgtctttgcagGAAGACACTTTCAACCAGAAAAGTAAGTGCAACTAGTGGGGCAGCTTCGGTTCCTGATGAGGTTTTCCACAGAGCCAAAGGGGTCCAGTTGTGCAATACT
















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|71330803|gb|DR802197.1|DR802197
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|5325047|gb|AI783238.1|AI783238
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|5846859|gb|AI999942.1|AI999942
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|14243528|gb|BG841239.2|BG841239
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|76285536|gb|DV025104.1|DV025104
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|24934412|gb|CA452630.1|CA452630
EST:     ACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCTTCGGT
genomic: ACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|71759578|gb|DR957515.1|DR957515
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|32851314|gb|CD990995.1|CD990995
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAACTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|101401376|gb|EB822365.1|EB822365
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|71446189|gb|DR827239.1|DR827239
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|5847487|gb|AW000566.1|AW000566
EST:     TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
genomic: TGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT
EST: gi|6448370|gb|AW181136.1|AW181136
EST:     AAAGCATGGCTCATGTTCAATG                         GAAGACGCTGTCAGCTAGAAAAGTTAGTGCAACTAGAGGGGCTGCCTCGGT
genomic: AAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGT

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: 47 (upstream exon), 48 (downstream exon)
Score: 31

TGTTACCTTGTATAGCATGTGGATCACGTGGATTAGTGACATGCAACACATGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 33

TGTTACCTTGTATAGCATGTGGATCACGTGGATTAGTGACATGCAACACATGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 23

TGTTACCTTGTATAGCATGTGGATCACGTGGATTAGTGACATGCAACACATGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 31

TGTTACCTTGTATAGCATGTGGATCACGTGGATTAGTGACATGCAACACATGTACTGGATATGGTTCCCTCCTTGCACAAAGCATGGCTCATGTTCAATGgtaatcttga ... ctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgttacagtaatcccctgatatatcgatccaactcgaactattctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA
               ccctgat  putative branch site (score: 31)
                                           ttctgtttcc  putative PPT
                  tgatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatatttattttatttaatagtttcaagaaatcacttcagattgctgttacagtaatcccctgatatatcgatccaactcgaactattctgtttccagGAAGACGCTGTCAGCTAGAAAAGTTAGTGCAGCTAGAGGGGCTGCCTCGGTCCCTGAAGAAGTTTTCCACAGAGCCAAAGGAGTGCAGCTATGCAACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT