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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaaatatttatttactacctagatgttaaatatattaatgtttatcttccaaattttatgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG

Basic information

species Zea mays
transcript GRMZM2G173700_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
gtaatcaaatatttatttacta---cctagatgttaaat-atattaatgtttatcttccaaattttatgt-accttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
|||||||| |||||| ||   |   | |  ||||  | | | ||| ||| ||   ||  || | | || | |     || | |||| |||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||| ||||||||||||||||||| |||||
gtaatcaattatttagttgaaaaatcatgcatgtggagttagatttatggtt--tttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15
gtaatcaaatatttatttactacctag-atgttaaatatattaatgtttatct-tccaaatttt---atg------------taccttttattttcttcca--gGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
      |||| |||||| |  |  |   |||| | ||   || |   || ||| |  | |||||   |||            |  |||| ||||| || ||  ||||  ||||| || || || ||||||||||| || ||| | || ||    |||||||| |||||  | || ||||||||||||||||||||||| |||||
----gtaaatctttattcatcatttgttatgtcacatgccttgaatcttttctatgtagattttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA13G33390.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------------------------------------------------gtaatcaaatatttatttactacctagatgttaaata--tattaatgtttatct-----tccaaattttatgtaccttttattttcttcca--gGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                                                              |   |    ||| | |||   || |  ||  || |    ||||  || |||  |     ||||  |   |  ||  ||| ||||| || ||  ||||| || || || || || ||||| || || || ||| | ||| |  |||| | ||| ||| || |||||||||||||||||||||| ||||| |||||
gtaaaatcatagtttatcatttcttaccttgccttgctagtatctaacacttcatgtcttgccttgctagtatgcacaaaagtgaaaaatccttgagtttctttatgtcttttggacttgtattctataccactatttctgattagataagattccatttgaaacatatgtttaattttattgcacagGTGGTCAGGCCAAGACACTCATGTTAGTCCAAATTAATTCAGATTTAAAGTCTTTTTCTGAATCTCTAAGTACTTTAAAGTTTGCTGAGAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
----------------------------------------gtaatcaaat--atttatttactacctagatgttaaatatattaatgtt-tatcttccaaattttatgtaccttt-----tattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                         || |    |  |||| ||| | |  | ||| ||||  |||||   ||  |  ||| | || ||    || ||||     |  | | |   |||||| ||||| ||||| || |||||||| ||| | |||||||||||||  |||||||| |||||| |||| || || |||||||||||| |||| |||||
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgc-attttgat-ttaagcatattgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
----------------------------------------gtaatcaaat--atttatttactacctagatgttaaatatattaatgt--ttatcttccaaatttta-----tgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                         || |    |  |||| ||| | |  | ||| ||||  |||||   ||  |    | | |||||  |     | |  |  || |  | ||  |||||| ||||| ||||| || |||||||| ||| | |||||||||||||  |||||||| |||||| |||| || || |||||||||||  |||| || ||
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatttgtttgc-attttgat-ttaagcatattgcagtcatggcttactaaattgcaatagctttgtcccttgtaattttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 15
--gtaatcaaatatttatttactacctagatgttaaat-atattaatgtttatcttccaaattttatgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
     || | |||    |  |  |   | || |||  | |||||  || ||   |    | |  |     | ||||| ||| ||  ||| || ||||| |||||||| ||||||||||| || ||||||||||  || |||||| | || ||| |||||||||| || ||||| ||||| || |||||
gtactataagatagacttcaataaaaaaaatattacttgatattgttgcttgcttctttactcct-----ctttttaatttttt--agGAGGGCAAGCGAAAACTCTTATGTTTGTTCAAATTAATCCTGATGAAGATTCATATGCTGAGACTGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 17
------------------------------------------------------------------gtaatcaaatatttatttactacctagatgttaaatatattaatgtttatcttccaaatttt-atgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                                      | || |||||  |||   || | ||  |     | || |  || || |  |  ||||| || | |   ||  |    | ||||||| |||||||| ||||| |||||||| ||| | |||||||||||  | |||| ||| ||||||  ||||||||| || |||||||| ||||| |||||
gtacttcactgttttccagttgcttttagcaataaatcccttcacctgtcttattgtttcgtcaggactctaaattatttccttagctccca-atagtcctctttttgaacttcatatagcggatttttattttctactttataaactacagGTGGTCAAGCAAAGACTCTTATGTTTGTGCAGCTTAATCCTGATGTGAATTCATTTTCTGAAACTGCAAGTACTTTGAAATTTGCTGAGAGGGTTTCTGG

upper sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------gtaatcaaatatttat-ttactacctagatgttaaatatattaatgtttatcttccaaattttatgt-accttttattttc------ttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
                                                || |       || |  ||   |  | ||  ||  |  | ||||  |||   | ||     || | | ||| ||| ||||       ||  ||| || ||||| || || || |||||||| ||| | ||||||||||| || || || || |||||||||||||| || |||||||| || || || |||||
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG

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|31354629|gb|CD438986.1|CD438986
EST:     TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT
genomic: TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT
EST: gi|31353200|gb|CD437557.1|CD437557
EST:     TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAG                         GTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT
genomic: TGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGT

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: 186

CTCTCTGCGTTAGGTGATGTTATTTTTGCTTTGTCACAGAAAAGTGCCCATGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 43

CTCTCTGCGTTAGGTGATGTTATTTTTGCTTTGTCACAGAAAAGTGCCCATGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 31

CTCTCTGCGTTAGGTGATGTTATTTTTGCTTTGTCACAGAAAAGTGCCCATGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

CTCTCTGCGTTAGGTGATGTTATTTTTGCTTTGTCACAGAAAAGTGCCCATGTGCCTTATAGAAACAGCAAGTTAACACAAGTTCTTCAAAGTTCTTTAGgtaatcaaat ... tttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatatattaatgtttatcttccaaattttatgtaccttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG
       tattaat  putative branch site (score: 82)
                                   taccttttattttctt  putative PPT
     tatattaatgtttatc  TA-rich tract