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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactacattgaatcccattgattttgcttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA

Basic information

species Zea mays
transcript GRMZM2G023289_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g50480.2 (Oryza sativa), 3'ss of exon 3
gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagca-ttgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactaca-ttgaa----tcccattgattttgcttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA
                                                                                                       || ||  | | |||||  |||  || || |  || ||  |    | | ||||   |  |||| |    ||| |    |  |||| |||||||||| || ||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||
-------------------------------------------------------------------------------------------------------atttattagtggttgtaatctatctcagttgtagattgctcttgaaagttggaactt-tgaattgtggttggagatttgacatttattttgcttggtatagATCATTACAAAAATGGCTGCCGCTAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGCCTCATGTCTACTCCAGCTGTATCTGCTGTTATCCGTGAAA

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 3
gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactacattgaatcccattgattttgcttg--ttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA
                                                                                            |||   |        || ||  |  | |  | |   |   |  | || | |  ||   |   | | |||     ||||      | | |||||||  |     | ||||| ||||| |||||| | || || ||||||||||||||||||||| |||| |||||  |  |  | || |||||||| ||||||||||| || |||||||
--------------------------------------------------------------------------------------------ttcttgtatgag---aggatattcatttcatgctacatcacatgcttgtcttctaatgtcaatat-catatttgacatca----ctaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAA

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 3
gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactacattgaatcccattgattttgcttg--ttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA
                                                                                            |||  ||        || ||  |  | |  | |   |   |  | || | |  ||   | | | | |||     ||||      | | |||||||  |     | ||||| ||||| |||||| | || || ||||||||||||||||||||| |||| |||||  |  |  | || |||||||| ||||||||||| || |||||||
--------------------------------------------------------------------------------------------ttcttatatgag---aggatattcatttcatgctacatcacatgcttgtcttctaatgtcgatat-catatttcacatca----ctaatgattttaatgaatctgcagATTATAACTAAAATGTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTACTTTCCACTCCTGCAGTATCTGCTGTTATACGTGAAA

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagttttt-ttaatagacttggtgttcatgaactacattgaatcccattg-attttgcttgtta-cagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA
                                                                                                     |  | | |  |  |   || ||     |  ||  |||  |  |  || |  ||  | |  |  ||| | ||  || | |||  ||||||  | ||| ||||||||||  || ||||| || || ||||| ||| ||||||| ||||||||  |||||| |||  | || |||||||||||||| ||||| || |||||||
----------------------------------------------------------------------------------------------------taagt-ttgtttgatctactcctattacaaatccggttcatactgttacagatgaagatgttttactgcttttcatacaattttattttgtatcttaacagATCATAATTAAGATGGCAGCAGCTAATGGTGTACGACGTGTGTGGGTTGGTAAAAACACTCTGTTATCAACTCCTGCTGTATCAGCTGTGATTCGTGAAA

upper sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 4
gtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactacattgaatcccattgattttgcttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA
                                                                                   |  |||| ||    || |  ||| |   ||| || ||      | | | |   ||| | ||||    ||  | || || || |   |  | |   ||  |   |||      ||||| ||||  || ||||| ||||| |||||||| |||  ||| |||||||| |||||  |  |  | || |||||||||||||| ||||||||||||||||
---------------------------------------------------------------------------------aaatccttgcatc---atccgaatg-attcttgatggctgtgttgtaatgcc---tttatctaatg---ttttttttaattaatttt-tctatttttataaaaactgc------cagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGTCAAAATGGGTTGCTTTCAACTCCTGCTGTATCAGCTGTCATCCGTGAAA

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|211503691|gb|FL022246.1|FL022246
EST:     CCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAG                         ATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGA
genomic: CCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGA
EST: gi|31351485|gb|CD435842.1|CD435842
EST:     CCATTGTTGTCTCTGGTGATGGCCGTTATTTCTCAAAAGATGCTGTTCAG                         ATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGA
genomic: CCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGA
EST: gi|211099119|gb|FL353128.1|FL353128
EST:     CCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAG                         ATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGA
genomic: CCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGA

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: 462

GTGCAACCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 474

GTGCAACCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GTGCAACCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 882

GTGCAACCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttaga ... cttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagacttggtgttcatgaactacattgaatcccattgattttgcttgttacagATCATAACAAAAATGGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAA
                                        ttttgctt  CT-rich tract
                                   attgatttt  TA-rich tract