Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttctgtttttccgtctacttttgtcaattttccttgtccatctaaataagctgctcaggtagatttaagcattcatttgacctggacactgacaaaaaaaaaaattgttatccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA

Basic information

species Zea mays
transcript GRMZM2G376727_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376727_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 5
gtatttctgtttttccgtctacttttgtcaattt--tccttgtccatctaaataagctgctcaggtagatttaagcattcatttgacctggacactgacaaaaaaaaaaattgttatccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAG---AGCAGCTCAAAAGGAA
                          || |||||  || ||||     |  | |||        | |  |||     | ||| |    | ||       |   | |||     |||||||| ||||||||||||||||||| || ||||| || ||||| |||||    || |||||| ||||||||||||| ||||| |||||||| ||    ||| |  ||||||   
--------------------------gtaaatttactctttgttttattctacaag------gagcaacttttctagtgcatctatggtagaagaaattactgagaaa-----ttatccatttgcagAGGCTTGTGGCGAAGTACGGGTCGCTGGTGTCCGTTGTTGGCTTGGTTGGAGTGTTTATCTACCTGGTTGCAAGCCCGTCAAAATCCAGCGGTGCAAAAG---
















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|211340832|gb|FL479597.1|FL479597
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15053451|gb|BI358996.1|BI358996
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|7135675|gb|AW498208.1|AW498208
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15590113|gb|BI674729.1|BI674729
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|21987232|gb|BQ778760.1|BQ778760
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|211130311|gb|FL066378.1|FL066378
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|32828788|gb|CD968466.1|CD968466
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|60354184|gb|DN221157.1|DN221157
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15215431|gb|BI431279.1|BI431279
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|30706031|gb|CD059006.1|CD059006
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15590464|gb|BI675080.1|BI675080
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|87156435|gb|DY401224.1|DY401224
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|60347341|gb|DN214314.1|DN214314
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|32829808|gb|CD969486.1|CD969486
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|149106143|gb|EE291820.2|EE291820
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|60347158|gb|DN214131.1|DN214131
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|31611983|gb|CD568605.1|CD568605
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|38671702|gb|CD219303.2|CD219303
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|74243940|gb|DT651854.1|DT651854
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|78081691|gb|DV510103.1|DV510103
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|7137614|gb|AW499182.1|AW499182
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|76285099|gb|DV024667.1|DV024667
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|211354953|gb|FL243593.1|FL243593
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|8930280|gb|BE225044.1|BE225044
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|9255123|gb|BE345591.1|BE345591
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|60346405|gb|DN213378.1|DN213378
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|78080233|gb|DV508645.1|DV508645
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|78107599|gb|DV526017.1|DV526017
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|5006027|gb|AI712089.1|AI712089
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|24769483|gb|CA404612.1|CA404612
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|211130310|gb|FL066377.1|FL066377
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15545702|gb|BI643496.1|BI643496
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|24765720|gb|CA400879.1|CA400879
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|37377085|gb|CF625114.1|CF625114
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|78080443|gb|DV508855.1|DV508855
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|211379488|gb|FL165247.1|FL165247
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|16919381|gb|BM074163.1|BM074163
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|60356569|gb|DN223542.1|DN223542
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|89249519|gb|DY621305.1|DY621305
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|37383348|gb|CF628683.1|CF628683
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|8666106|gb|BE186922.1|BE186922
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|15590463|gb|BI675079.1|BI675079
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG
EST: gi|60355754|gb|DN222727.1|DN222727
EST:     AAGAAGTTTGAATGGGCTAAG
genomic: AAGAAGTTTGAATGGGCTAAG

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: 41 (upstream exon), 49 (downstream exon)
Score: 224

GCTAAGgtatttctgt ... ccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 235

GCTAAGgtatttctgt ... ccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 300

GCTAAGgtatttctgt ... ccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 174

GCTAAGgtatttctgt ... ccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcattcatttgacctggacactgacaaaaaaaaaaattgttatccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA
                    cactgac  putative branch site (score: 174)
                       tgacaaaaaaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttctgtttttccgtctacttttgtcaattttccttgtccatctaaataagctgctcaggtagatttaagcattcatttgacctggacactgacaaaaaaaaaaattgttatccatgtgcagAGGCTTGTGGCGAAATATGGGTCACTTGTGTCTGTTGTCTCATTTGTTGGATTGTTTATCTACCTCGTTGCGAGCCCGTCGAAGAGCAGCTCAAAAGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA