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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag

Basic information

species Zea mays
transcript GRMZM2G323622_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g54080.1 (Oryza sativa), 5'ss of exon 14
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaag-acggcag-------agctcaaaatag-aaagttgaattgataatagtcgt-ggcgatattagtaattggtgcctgacattgttttttttcctag
 ||||| |||||||| ||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || ||||||||||||   ||  | |       |  |||| | || |||  ||   || |||   || | || ||||||   |||||    ||   ||  ||||      |||
TTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATACACAATGgtatttactactgtttaactaattcaagacagcaaacctgctctgctaactatcattggggatattgtaaattgac-tctcttatc-ttttaccctttag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G35130.1 (Glycine max), 5'ss of exon 12
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgata-atagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
|| |||||| || ||  |  | || ||||||||||| ||||||| ||||||||| || ||||| ||||| |||||||||||||| || ||||| ||||||||| ||   |   |   ||| |   |  || |  | ||| ||  |  |   ||    | |  |   |   | | ||       ||||  ||
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACAATGgtatgaaccctctgaataaatt--gatttttatctcatacatcatgttattgaaggaattcttcattctataagatgccaacctttctcag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G01800.1 (Glycine max), 5'ss of exon 14
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
||||   || |  || ||  ||||  |||| |||||||||||||  ||||| || || ||||| |||||||||||||| || |||||||| || || |||||| | |   | | |            ||| |||   |  ||   || |||    |||       | | |  ||     |||| | ||||
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATATACGATGgtatg-cattatatcc-----------gtttaatgcttttta--tgttgcgtatctagcctaatttacttagcaactgcttttctactag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G37800.1 (Glycine max), 5'ss of exon 14
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattag-taattggtgcctgacattgttttttttcctag
||||   || |  || ||  ||||  |||| |||||||||||||  ||||| || || ||||| ||||||||||| || || |||||||| || || |||||| |           ||  |||    ||| |||   |  |  |  ||   || ||   |||||  | | |  || |   |||| | ||||
ATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATATACGATGgtatg-----------cattatattc-gtttaatgcttttttatgttgcgtatcttgtctaatt--tacttagcaattgcttttctactag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G33390.1 (Glycine max), 5'ss of exon 10
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
 |   |||| || ||  |  | ||  ||||||| ||||||||||||||||| || || ||||| ||||| || ||||||||||| || |||||||||||||||||       | ||  | ||| | |  | | |    | |     |   |  |||| | |||      | | ||    || |||| |||
GTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTACACAATGgtaagc------aactttatatatatatatcattcatcattttagataaaggaattactcatt---ctataagatgtcattatttcttag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G10190.1 (Glycine max), 5'ss of exon 13
--ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
   |    ||| || ||   | | ||  ||||||| |||||||| |||||||| || || ||||| ||||| || ||||||| |||||| |||||||||||||||||       |  |  | | | | | |||| || |   || |  | ||  | ||||                                
GTGTATGTTGAAATACAAGATTTTATACGATCAGTGCTTGATGGCTTTAATGTATGTATATTTGCTTATGGCCAGACTGgtttaggaaaaacttacacaatggtaagcaactttatattcacacatata-ttgattttaatttaat--tcgccgtcttag--------------------------------

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G04580.1 (Glycine max), 5'ss of exon 6
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaat-tgata-atagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
|| |||||| || ||  |  | || ||||||||||| ||||| | ||||||||| || ||||| ||||| |||||||||||||| || ||||| || |||||| ||   |    || || |||   | ||  || | ||| ||  |  |   ||    | |  |   |   | | ||      |||||  ||
ATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTATACGATGgtatgaaccct---ctgaatatattgatttttatctcatacatcatgctattgaaggaattcttcattctataagatgccaacttttctcag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 13
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcc--tgacattgttttttttcctag
||| || |||||  | ||||| ||  ||||||||||||| ||||  ||||| || || ||||| |||||||| || || ||||| || |||||||||||||||      ||      |  |||  | | | || ||   | |    ||  |  | ||   |||  | ||  |  |||||||||| | |    
ATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTACACAATGgtactcattca----ctagtatatcacgattaagtggccagacaaatgatgccactac--attcataccattatcattgtttttgtccag--

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 5'ss of exon 14
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag-----
 ||||  ||||  |  ||  | ||  ||||  |||||||||| | |||||| || || |||||||||||||| |||||||| ||||| ||||| |||||||||| |   || ||||  |  | |    || |   |||| |  |     | ||  |  ||| |  |  || ||| | | | |||| | |      
TTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTATACAATGgtaa-attaca-agcttgattttg----ttaa--cgata-tgctttaaccaatgattataagtttt-tctaacagtttctattttgcaaacacag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 13
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaaga--cggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
 || ||||| |  || ||  || |  |||| ||||||||||| | |||||| || || ||||| ||||||||||||||||| || ||||| |||||||||||| ||    | | |  |   | |  | | | | ||   |  |  |  |  | |||     || | |||      ||||| |||  || |||
GTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATACACAATGgtatgaacttgtatatgttttagtctaca-tggcatatgtgttgatattttcaata---aaaacttgtgtaatgtattgtctttcctc-tag

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ12333 (Selaginella moellendorffii), 5'ss of exon 9
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaag-acggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
||||   ||||  |||||  ||||  | |||||||||||||| |  || ||||| |||||||| ||||||||||| || || ||||| || ||||| ||||||   | | || |    | || |  |   |       || | |  ||   |                                       
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtatttatgacatattatacaacaacattatttgcaactatttgctgtacag---------------------------------------

upper sequence: GRMZM2G323622_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ19920 (Selaginella moellendorffii), 5'ss of exon 9
ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaag-acggcagagctcaaaatagaaagttgaattgataatagtcgtggcgatattagtaattggtgcctgacattgttttttttcctag
||||   ||||  |||||  ||||  | |||||||||||||| |  || ||||| |||||||| ||||||||||| || || ||||| || ||||| ||||||   | | || |  |  | | |  ||  | | |||  | || | |  |                                         
ATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTACACCATGgtatttatgacataatt--atacaacaacattatttgcaactatttgctgtacag------------------------------------

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|211110697|gb|FL352656.1|FL352656
EST:     TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATG                         AGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
genomic: TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
EST: gi|211353939|gb|FL310943.1|FL310943
EST:     TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATG                         AGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
genomic: TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
EST: gi|38687291|gb|CK144322.1|CK144322
EST:     TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATG                         AGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
genomic: TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
EST: gi|211021362|gb|FL343609.1|FL343609
EST:     TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATG                         AGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA
genomic: TGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTA

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: 466

ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTTTATATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 80

ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTTTATATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTTTATATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

ATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTACACAATGgtaagacggc ... tttttcctagAGTGGGCCAGGCACATCAAAAGAAGATTGGGGTGTTAACTATCGAGCTTTAAATGACTTGTTTTATATCTCTCTAAGTAGAAGGAATGCTTTCTCATATG