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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaggttgtgtcaagcgaacaatgttttcaacttttgatgatggcagatggctcaaggacacgccttctgttccttgatcttgtaaacaatgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA

Basic information

species Zea mays
transcript GRMZM5G824843_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 14
--------ctaggttg-----tgtcaagcgaacaatgttttcaacttttgatgatggcagatggctcaaggacacgccttctgttccttgatcttgtaaacaatgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA
        |||| |||     |||| ||| ||||||  | | || |||| ||           || |  |||    ||||||||  | ||| | |||  | ||| |   |||||||||||||||||||||| || ||||| || ||||||||||||||||||| ||  ||| |||||||||||||||||||||||||||||||||| |||| |
ttcctgaactagattgctctttgtccagcaaacaatactataaaattttcata----------gcacttggaatgtccttctgtctcctgagcctgtttataatat---ccagGTGTGTCTTTGTTGATGCGGGTGTGGCTGCCATTGACATTGAAACAAAAAAGAGGAAAGAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCGGCTGCA

upper sequence: GRMZM5G824843_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0056g00040.t01 (Vitis vinifera), 3'ss of exon 18
-ctaggttgtgtcaagcgaacaatgttttcaacttttgatgatggcagatggctcaagg-acacgccttctgttccttgatcttgtaa-acaatgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA
  |||   |     || ||   |   |   ||    | |  |    ||||   |  | | |||    |  ||||   |    |||| |  |  |||||  ||||||||| ||||| ||||||||||| ||| | |||||||| ||||||| || ||| ||| | || |||||| ||| ||| || | |    | || | ||  
tttagaaaggccttagagagagaaaataaaaa---ataaaaagaagagatattttgaagtacaacaatattgttatatctgtttgttatgctgtgtttttcagGTGTGTTTTTGTGGATGCTGGAGTTGCACCTATTGACATAGAAACAAGAAAGATGAAAGAGGAGATGAAATCAAAAGAGGCACGGGCAAGAGCTGTTGCT
















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|31364251|gb|CD448606.1|CD448606
EST:     GCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: GCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
EST: gi|211541873|gb|FL034149.1|FL034149
EST:     TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
EST: gi|211541872|gb|FL034148.1|FL034148
EST:     TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
EST: gi|211538865|gb|FL034144.1|FL034144
EST:     TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
EST: gi|71428569|gb|DR809619.1|DR809619
EST:     GCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: GCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
EST: gi|211541869|gb|FL034145.1|FL034145
EST:     TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
EST: gi|211541870|gb|FL034146.1|FL034146
EST:     TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGA                         GTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG
genomic: TTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAG

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: 168

GGCCCCAATTTAGGTACCTTGGAGATGTTTCAATTCCCTTTGCAACTGGTGCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GGCCCCAATTTAGGTACCTTGGAGATGTTTCAATTCCCTTTGCAACTGGTGCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GGCCCCAATTTAGGTACCTTGGAGATGTTTCAATTCCCTTTGCAACTGGTGCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

GGCCCCAATTTAGGTACCTTGGAGATGTTTCAATTCCCTTTGCAACTGGTGCCGTTTGGCATCGAAGGCAGTTATTTGTGTCTACACCAACAACAATTGAgtaagatttt ... tgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatggctcaaggacacgccttctgttccttgatcttgtaaacaatgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA
                           ccttgat  putative branch site (score: 123)
                                             tgtttccc  putative PPT
                                      taaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaggttgtgtcaagcgaacaatgttttcaacttttgatgatggcagatggctcaaggacacgccttctgttccttgatcttgtaaacaatgtttcccagGTGTGTCTTTGTTGATGCTGGAGTGGCAGCGATTGACATTGAAACAAAAAGGATAAAACAAGAAATGAAAGCAAGAGAAGCTCAGAGTCGGGCAGCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - gaacaat
- - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - -gcagatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaaacaa