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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttgttttctttatattctgttattatggtgcaaaattggatatctaacttggctaactccactcactctttttaattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG

Basic information

species Zea mays
transcript GRMZM2G000749_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 10
gtattgttgttttctttatattctgttattatggtgcaaaattggatat-ctaacttggctaact---ccactcact--------ctttttaattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG
||| || || ||| |||      |||| ||| ||  ||  | | ||| |  ||  ||||||||||    |  ||| |        || || ||||||||||||||| ||||||||||||||  || | | || |||||||| ||||||||||||||||||| ||||||    ||||| || | | | |    ||   | ||
gtactgctgatttattt-----ttgtttttacggcacaggacttgatgtattagtttggctaactaactctttcatttccaccccctattgaattcaaaagCAAAGAAGATGCCTACAGATACTGCAGAGTTAAAAAGAATGGTGAAATCAAAATATCCATTTGTTGATGAAAATCTGGACCAAGTCGTAGGCATCATATG
















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|21987416|gb|BQ778944.1|BQ778944
EST:     AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG                         CAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
genomic: AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
EST: gi|211021453|gb|FL457596.1|FL457596
EST:     AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG                         CAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
genomic: AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
EST: gi|60341236|gb|DN208209.1|DN208209
EST:     AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG                         CAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
genomic: AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
EST: gi|149097304|gb|EE183133.2|EE183133
EST:     ACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG                         CAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
genomic: ACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
EST: gi|71761192|gb|DR959129.1|DR959129
EST:     CAAATAAGGCTTTAATTGAGATAG                         CAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
genomic: CAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA
EST: gi|22543109|gb|BU093547.1|BU093547
EST:     AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAG                         CAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGCGAAATCAA
genomic: AGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAA

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: 93

GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GCTCTACATGAGTGGAGAGATCGTATAGCTCGTCAGGAAGATGAGAGTACTGGTTATATACTGCCAAATAAGGCTTTAATTGAGATAGgtattgttgt ... aattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaattggatatctaacttggctaactccactcactctttttaattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG
                                     ctcttttta  CT-rich tract
                                      tctttttaattcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttgttttctttatattctgttattatggtgcaaaattggatatctaacttggctaactccactcactctttttaattcaaaagCAAAGCAGATGCCTACAGATGTTGGACATTTGAAAAGAATTGTGAAATCAAAATATCCATATGTTGAGAGCAATCTTGAGCTAATTGCTTACACTGTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA