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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag

Basic information

species Zea mays
transcript GRMZM2G164352_T05
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA07G10000.1 (Glycine max), 5'ss of exon 7
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
||| ||||| || ||| | || |||||||| ||| | ||||||||||| |||||||||||  | || || || |||||||| ||||||||||| || |||||  ||  | |    ||   ||||   |    ||| |    | | |   ||| | |     | | | || ||| ||| |||  ||  | |||   | |||     |||  |  | |||  |                                                                  
TACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAGgtttgtggcttaaaattgaatattccttcagattgac----catgtacatttcaaac----attattatttttcatatgctccct--ctattg--aagcttatgatttacacatggattgcag----------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA02G10790.2 (Glycine max), 5'ss of exon 8
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 || ||||| |||||| |||| ||||| |||||  | ||||| || |||||||||||||| || || || || || ||||| ||||||||||| ||||||||  |||  |  ||||  ||  ||   | |||||||   || ||||      || | |||  |     |  |||      |   |  |  |    |||||     || |                                                                              
AACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGAATCAGgtttgtag-agcttttgagtggtt---tctatttgcaaattgcttta-----taaactttcgacaaccttgtttcctttttgtttttctctggtaatgctgttaattct------------------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G24790.1 (Glycine max), 5'ss of exon 8
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 || ||||| |||||| |||| |||||||| ||  | ||||| || ||||||||||| || || || ||||| |||||||| ||||||||||| ||||||||   |   || |||| ||| ||||  || ||||        ||   || ||||||||| |  ||  | | ||| |    |  ||  |   |  |||  |  ||| |   |                                                                            
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgt---tgttatattttctgtaattaatttaattt-------tctgaatgctttagatttcttttggcaacctttgttccttttct--ctgctgatataattaattctagcat---------------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G42250.1 (Glycine max), 5'ss of exon 8
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 || ||||| |||||| |||| |||||||| ||  | ||||| || |||||||| || || || || ||||| |||||||| ||||||||||| ||||||||   ||   ||| | | ||||    ||||| ||      | |    || ||||||||| |  ||  | | |||      |  ||  |   |  |||  |  |||     |                                                                            
AACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGAATCAGgttgttatagtttctgtagtta----atttaatt------ttcagaatgctttagatttcttttggcaaccttttctcctttcct--ctgctgatataattaattcgagcat---------------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G31760.1 (Glycine max), 5'ss of exon 8
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 || || || || ||| | || |||||||| ||| | ||||||||||| |||||||||||  | || || || |||||||| ||||||||||| || |||||  ||  | |    ||   ||||   |    ||| |    | | |   ||| | |     |   | || ||| ||| |||  ||       ||  ||  |  |     | | |||  |                                                                    
CACAATCGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGAACCAGgtttgtggcttaaaattgaatattcattcaggttgac----cgtgtacatttcaaac----acaattatttttcatatgctccctctattgaagcttgtgatttacacatgaattgcag--------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 8
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgt-tattagatttatttgcctt-ttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 |||||||| || ||  | |||||||| || ||  | |||||||| |||||||||||||| || |||||||| || |||||  | |||||||| || |||||  ||  ||| | | |||| |  |  |  || |    || || ||| ||  ||||| |  | | || | | | || || |  ||                                                                                                        
AACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCAACCAGgtttgttgcatctctcttgtgtgctttagatactacttttattgcttccttatttagttggtgactgaattatcttttacggcag--------------------------------------------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 8
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtc--cttgaaagccttgcctttctcttcaaaattatc-tgatgatt-gctgatttttgttttgatctttcag
 || ||||| || ||| ||||||| || || ||| | ||||||||||||||||||||||| ||  | ||||| |||||||||||||| ||||| || |||||           ||  | ||     | ||| |   || ||  |  |    || | ||| || | |  ||    ||   | |   |||  | |  ||| |    ||  | ||||  ||| |  ||||| |||     |||| ||     | || || | |||||| | |  |||||  ||  |  |  |||
AACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAGgt-----------ttgctattgaccaagttactcatctctttgta-cgacattgggtttcta-ttttttcccacatgttcaaaggagctgt-atcatgtt----ttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccag

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 5'ss of exon 7
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 || ||||| || ||| |||||||||| || ||| | ||||| || || ||||||||||| ||||| || || || ||||| ||||||||| | ||||||||   |  |||  |||  |   ||  |   ||  ||||||   |||   |||||  |  |     || |  |       ||||| ||| |||      |||  |||||| ||    || |                                                                   
AACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAATCAGgtt--tgtcataatttaaggagtttca--catcagccttt---ttttaattttatgtgctctgcctacttgt-------ctagccagctatt------ctactttttttaaatgcaattt-------------------------------------------------------------------

upper sequence: GRMZM2G164352_T04 (Zea mays), 5'ss of exon 8
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 5'ss of exon 9
TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtaccatttttt-ttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtccttgaaagccttgcctttctcttcaaaattatctgatgattgctgatttttgttttgatctttcag
 || || || || ||| | || |||||||| ||| || | ||||| || ||||||||||| ||||| || || |||||||| ||||||||||| || |||||  ||   |||||   |||| |||   |   |||   || | |    || ||       |  |||     || | | ||    | |   ||||  | ||                                                                                        
AACAATAGATCAACTTCTGCCCATTTTCCTTTCTCTGCTTAAAGATGAGTTTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAAACCAGgtttgtctgattttccattgtcatttcttggttttcatttgttccagttggttagagaggtagatggttggttctgttaga-gaccacttattaaaaggca---------------------------------------------------------------------------------------

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|87156353|gb|DY401142.1|DY401142
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67016540|gb|CO445289.1|CO445289
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|87157118|gb|DY401907.1|DY401907
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|31362531|gb|CD446888.1|CD446888
EST:     CTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: CTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|26558526|gb|CA830761.1|CA830761
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67017790|gb|CO446539.1|CO446539
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|32933390|gb|CF038202.1|CF038202
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|22546073|gb|BU098394.1|BU098394
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|42491785|gb|CK700831.1|CK700831
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|23357737|gb|BU645386.1|BU645386
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67022121|gb|CO450870.1|CO450870
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|211315613|gb|FL415838.1|FL415838
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCARGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|26560084|gb|CA832319.1|CA832319
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|67039515|gb|CO465770.1|CO465770
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
EST: gi|13315895|gb|BG410243.1|BG410243
EST:     TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAG                         GTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA
genomic: TTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAA

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: 298

TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 213

TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

TACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTAATCAGgtcagtacca ... gatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA