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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT

Basic information

species Zea mays
transcript GRMZM2G178822_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT
                                           ||||  ||| || |     |   | | ||  | |  || || ||  |   |    || ||| ||||||||||  |||||||||||||||| || |||||||| |||||||||||||||||||| |||||||| ||||| ||||||
------------------------------------------gtaac-tttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT
             ||| |   | ||   |  || |  |  |||  | ||  ||   || ||| | |    ||| ||  |   ||||   | |  ||    |     ||| | |||||| |||||||||||||| ||||| || ||||||||||| ||| | || || ||||| || | ||| ||||||
------------gtgagtatttgttgcagaagcctgaag-ttactatacccctcttttttactg-tcaaatatctttaaggtttttcttccttccgtgaac----acagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 1
gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgcctta-tcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT
                   |  ||||   || || || |   | ||       |||| |  |   || | |||| |   || |||||     | |  | |||     ||| | |||||| |||||||||||||| |||||||||||||||||||| ||| | ||||| ||||| || |  || ||||||
-------------------gtgatttc--tttctctttttgcagaagttactatagtccccc---ttgtttattgttagttttttttattaaaattacctgcaaatacagGTACAAGTTAATTAAGGAAGTTGGTGATGGGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT

upper sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 1
gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatt--tttgccttatcgcat--gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT
                            ||   |    |  |||   ||||  | |||    |   | | |||||||   | ||  | || || |  |  |  ||||   ||| |  | | | || ||||||||||| |||||||||||||| ||||| ||||| || || ||||| |||| ||| ||||||
----------------------------gtgagtgggcttgtatggaacttgcttgtt----aatatttgtattttaatgtgttgatatgtctgagagttttggcctctacagGTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTT

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|211443458|gb|FL042456.1|FL042456
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443465|gb|FL042463.1|FL042463
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443464|gb|FL042462.1|FL042462
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211441336|gb|FL042450.1|FL042450
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443461|gb|FL042459.1|FL042459
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443466|gb|FL042464.1|FL042464
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443460|gb|FL042458.1|FL042458
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211443457|gb|FL042455.1|FL042455
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGANGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|211441339|gb|FL042453.1|FL042453
EST:     TGAAGGGTAAAACTTGCACNAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
EST: gi|113748605|gb|DW871977.1|DW871977
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGG
EST: gi|211443463|gb|FL042461.1|FL042461
EST:     TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG
genomic: TGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCG

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: 385

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 195

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 124

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

CAAACCCTTGCCTTTCGTGTCTGTTCATATTTCTCGTGGCTTGGTTATTCTGAAGGGTAAAACTTGCACAAGGCAGCTTTGATATTACAACAATGGATAGgtaactttta ... gccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT
                                            tgccttc  CT-rich tract
          attctctattttagat  TA-rich tract