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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag

Basic information

species Zea mays
transcript GRMZM2G075719_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaaca-atgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
||||||||||||||||||| | ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||| |||||||||||||   ||||||     |    || ||||        |||   |      |  || || | | | |    || || | ||| || |  |  ||  | ||                                                                      
GGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAAgtatgttctctcatctccatgtgcgcacatgggtg-gcatgtgtgttctcactaactgcttttatactagcaacaat-gcagcagaccaacagagaattgcc-------------------------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G04330.1 (Glycine max), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
|||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || || ||||| |||||||  |||||||||||||     | |  |  || ||  |             ||   ||||                |   ||| ||  | | |   | ||   ||    ||||| ||||||||  |      |  | |                                            
GGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAAgtacgtcatttgggattcgctttctttt---------cacctttta----------------ctattgcccactatttgatgctatc-ttacatggttttgtcttttaataaaagttaatctgatc------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
|||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || |||||||||||||| |  |||||||||||||  |  | |    ||   |      ||     ||   | | | | || |||  ||  | ||   ||||  |   |     || | |  |  |  | |||    |||                                                            
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccattttgacctactttcttttca-----actattccctcatgacaaattatattttc--ttgcaggtttttcatttca-ttataataatatattaatagtta------------------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G16200.1 (Glycine max), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
|||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || |||||||||||||| |  |||||||||||||  |  | |    ||     ||   |    ||  |    ||  | ||  ||  ||  | ||   |||| ||   |     |||| |  |  |  | |||    |||                                                            
GGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatttagacct-----gctttctttcacctattccctccatgacgaattatattttc--ttgcagatttttcatttcaat-ataataatatattaatagtta------------------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G41100.1 (Glycine max), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgta-atctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
|||||||||||| |||||||| || || ||| | ||||||||||| ||||| ||||| || || ||||| |||||||  |||||||||||||  ||  |    || |   |    | |||     |   | || | |   |  |  || |   |  |  ||||   |     |  | | ||  |   || ||||  |                                                             
GGATACAGCTGGGCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATCAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAAgtacgtcatttggggtttgctttcttctcac-----cttttactgttgcccactatttgatgctatct-tacatggcttttgccttttaataaaag--ttaatctgat-------------------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcag-atgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttt-tactattttattcttacctttatttgtttcatgttgtag-----
|||||||||||| || ||  | ||||||||| ||||||| ||||||||||| || || || |||||||| ||||| |  |||||||||||||      |  |  |||  || | || ||| |   | ||| |     |    | ||  |       ||    ||||||     |   | |     ||||    || |     ||| |   ||  ||| |    | |   | ||     ||  |||||||     ||        
GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAAgtatgtgtaccttcactcgttctctcaaacacatgaatattttcccatatctgagatcttggggatgtggttttcagtaatcttatgaatttatgcgtttcgatttcttc--tttatgttgatccattgtgcgttgtgaaactcgagatttattttgttttccactgacatatag

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgta-atctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
||||||||| || |||||||| ||||||||| | ||||| ||||| || || || || || ||||| ||||||||||  |||||||||||||       || | | |||||  ||               |  ||  ||| |    | | ||   |     || | |   |    || ||     |  |  |                                                                  
GGATACAGCCGGGCAGGAAAGATTCAGGAGTCTCATTCCGAGCTACATTAGGGATTCATCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgaaatcctttatttctctgccatctttcttttttggcttctt--gaatagtttttgcattgtagatg-attattctaattgttgcctgatgggcatgtt------------------------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 5'ss of exon 3
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
|||||| || || |||||||||||||||||| | || ||||| || || || ||||| || ||||| ||||||||||  |||||||||||||  |  | |  |  | | |    ||               ||  |||||||   |  |     || ||  ||  |  |         |  |      |  |||||  | | |                                                      
GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAAgtatgcatttttcgcttttattttcca---------------ttatggaaaaatgtttctcatctattcatgtctttttctttctctcttttgtttccctcccttttgggtactt-----------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
|||||| ||||| ||||| |||||||||||||||||||| || || ||  | || || || || || ||  |||| | ||||||| |||||||   |      | | | |  || |     |      ||| | |   |     | ||  |  | |    || |||| ||  |||   |     | | || |                                                                 
GGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAAgtaagtac-----atttttgtgacaaaagaggaattttgttcctcacacagttgtacgg--ttggctcagtattagta-cattaattgtttcactgatgtaacacggg------------------------------------------------------------

upper sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctc-tcgcacacacaaacacacattctttaggaaaaaaaatggtatcagat--gcacatcagtagcaacaatgac-taggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag
||| |||||||| || || |||||||||||||||||||| ||||| ||  ||||||| || || || ||  |||| | ||||||| | |||||  | | | | |    | | | |   |    |   | |    |||          |  |    ||  ||   | | |||   || |||| ||  |||                                                                        
GGACACAGCTGGACAAGAGAGGTTCAGGAGTTTAATTCCCAGCTACATTCGAGACTCGTCTGTGGCAGTAGTTGTTTACGATGTTTCGAgtaag-tatatatataaggcattgtaaggagtttcgttcttcacctagctgtgctgtggtcactgtattcgcgtgttaatagttgcattgacataacaaga-----------------------------------------------------------------------

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|32836609|gb|CD976287.1|CD976287
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|211109341|gb|FL282964.1|FL282964
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|32840351|gb|CD980032.1|CD980032
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|32839843|gb|CD979524.1|CD979524
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|211109340|gb|FL282963.1|FL282963
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|30088223|gb|CB886428.1|CB886428
EST:     CGATG-TGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCNCTG
genomic: CGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
EST: gi|116822600|gb|EC866010.1|EC866010
EST:     AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA                         GCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG
genomic: AAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTG

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: 190

GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 352

GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctc ... catgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT