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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT

Basic information

species Zea mays
transcript GRMZM2G069765_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgta-tttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT
     ||| ||| ||  |  |||    |   |  ||      |   || |||||   |||    ||||||||| | || | | ||| || ||||||||| |||||||| ||||| |||||| | ||||| ||||||||||||||||||  |||||| |||||||| |                            
---gtattgcttgatcatt-gtatcagatggtgttatttcctttgttgattttttagtctg---ttctgaaacatttagtgtctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC----------------------------

upper sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
--------gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT
         ||   ||   |  |  |||||| | | ||     | ||||  |    || |||||||  |||    ||||   |  | |||| | || | |||||||| |||||||  | || |||||||||||||| |||||||||||||||||| || |  |||   | ||||                            
gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataaa--attgtttatat--taa----tgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC----------------------------

upper sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G28650.1 (Glycine max), 3'ss of exon 7
--------gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT
         ||   || || | |  |||||  | | ||     | ||||  |    || |||||||  |||    ||||   |  | |||| | |||| ||||||||| ||||||  | || |||||||||||||| |||||||||||||||||| || ||||||   | ||||                            
gtaacttaatagtgttactgt-taatcagtgtttctctcctacaaggtataaa--attgtttatat--taa----tgaatgctacaattttgtaatctgcagCATATAACAAAGCTTTGGAGGATGCTATTGCTGTCCTTGACAAAATTGCAATGCCTATTGATGCTCAGGATC----------------------------

upper sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 6
gtaagattccttta-ttctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT
     ||||    | ||    ||    |   |  ||| | |  ||  |     || | | || | |   ||||||| ||||| |  | |    |||||| |  ||||| || || |||||||||||||| |||||||||||||||||| |  | |||||||| || |                            
---gtattctagaaattgattgtgacacgactctctaagttgttaaattaaacttctcttttgattatggaaactt-tatttgttgtgt----agCATACAATAAAGCTCTGGAGGATGCTATTGCTGTGCTTGACAAAATTGCAATGTCCATAGATGTGAAGGACC----------------------------

upper sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 6
gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttctta--tcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT
|||| |  |||  ||     ||  || |   ||||    |  ||   ||  |||| || |||  ||    || ||  | ||    ||  ||| |||| ||||  ||||| ||||| ||||||||||| || |||||||| ||||||    |||||||||||||||| |                            
gtaaca--cctcaat-----gtgttgtaaagtactcatatt-tattggtgatttaaattttattttgatcaatttaaaattgaggtacttctgcagCTTATAATAAAGCTCTTGAGGATGCTATTGCGGTGCTTGACAAGATTGCAGCCCCTGTTGATGTGAATGACC----------------------------

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|149105498|gb|EE291023.2|EE291023
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211229383|gb|FL136771.1|FL136771
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAA-TTGNCA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTG-CA
EST: gi|211231450|gb|FL136786.1|FL136786
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAAT-GCA-
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211229385|gb|FL136773.1|FL136773
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|31354522|gb|CD438879.1|CD438879
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|211229386|gb|FL136774.1|FL136774
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCCACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGAACAAA-TTGCA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGA-CAAAATTGCA
EST: gi|22491088|gb|BU051011.1|BU051011
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|22491149|gb|BU051072.1|BU051072
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA
EST: gi|149084479|gb|EE173941.2|EE173941
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTTGACAAA-TTGCA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTT-GACAAAATTGCA
EST: gi|19351773|gb|BM896305.1|BM896305
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGGTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGGACTTGACAAAATTGC
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGC
EST: gi|211229388|gb|FL136776.1|FL136776
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAA
EST: gi|211229381|gb|FL136769.1|FL136769
EST:     TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAG                         CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAAT-GCAA
genomic: TGCACAGGCATTCATCGACAAGAACTACCATCCAACTGTTATTTGCCGAGgtaagattcc ... ttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT
                  tcttaac  putative branch site (score: 2)
                                     tatttttcttatcttc  putative PPT
         ttttttatatcttaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT