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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatctccctgtcgctgtgtatatgtgcatacagcggtgtgctgcagctctttcctgtgacactttgtctaaccatcttaaaaaccacctatattcattttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA

Basic information

species Zea mays
transcript GRMZM2G070422_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 7
gtacaatctccctgtcgctgtgtatatgtgcatacagcggtgtgctgcagctctttcctgtgacactttgtctaaccatcttaaaaaccacctatattcattttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA
||| | |  | ||| |  | |   | ||||| ||| ||   ||| || |  | ||  |  | ||   ||       || || ||  | ||||||  |   |||   ||||||||| || ||  | ||||| || ||||||||||| |||||||| ||| | || ||||| ||||||||||  || || ||||||||||||||||||||||
gtatagtgcctctgcctatattcctctgtgcttactgcta-gtgatgaaattattgtccat-acgtgttacgctttcaact-aatgatcacctacctctgttt---gaagGTAACAAAACCACTATTGGAGACATCAAGAAGAGGGTATCTTGCTGCACTGTCAGCATCGAGTTACTCCTTCGTCTCTTTGCTTCAGCACTTCCTTCCTA

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 7
gtacaatctccctgtcgctgtgtatatgtgcatacagcggtgtgctgcagctctttcctgtgacactttgtctaaccatcttaaaaaccacctatattcattttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA
                     ||| |  |  || ||    |  ||        | |  | ||| | || || ||     ||| || |  |  || | ||   |  |  |||| || || || |||||||| || ||  | | ||| |||||||| ||||| |||||||| ||||||||||||||||| || ||  |||| || ||||| |
---------------------gtaca-ataaattcattaataagcattgaagttcttttatga-atttggtata--tgactttaataaaaagtaaactc---tgatatagGTGACCAAACCATTGTTGGAGACATCTCGGAAAGGATATCTTGCTGCAATATCTGCATCTAGTTACTCCTATGTTTCTTTACTCAAGCATTTTCTTCCAA

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 7
gtacaatctccctgtcgctgtgtatatgtgcatacagcggtgt--gctgcagctctttcctgtgacactttgtctaaccatcttaaaaaccacctatattcattttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA
                                ||| |   ||   | ||      | ||   ||||  ||  | |    |  ||| ||      || |    | ||    |||| || |||||| ||||||| || || |||| ||| |||||||||||||| |||||||| ||||||||||| ||||| || ||  ||   ||| ||||||
-------------------------------gtactgttttgctggttgtgatcttatcagttgaccattcattttggtactttacaag-----taaacatctcttaaatagGTGACCAAGCCTCTGTTGGAGACATCCAGAAAAGGTTATCTTGCGGCAATATCTGCATCAAGTTACTCCTACGTTTCTTTACTCAAGTGTTTCATTCCTA

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|67015153|gb|CO443902.1|CO443902
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|211267877|gb|FL003942.1|FL003942
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|211267881|gb|FL003946.1|FL003946
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31361470|gb|CD445827.1|CD445827
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|32914780|gb|CF019592.1|CF019592
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCGAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|67017641|gb|CO446390.1|CO446390
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAAGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31356384|gb|CD440741.1|CD440741
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|67019739|gb|CO448488.1|CO448488
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAAGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31357208|gb|CD441565.1|CD441565
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31362224|gb|CD446581.1|CD446581
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|67042246|gb|CO468501.1|CO468501
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|84980240|gb|DW530589.1|DW530589
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|9952049|gb|BE638632.1|BE638632
EST:     GCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: GCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|6526869|gb|AW216132.1|AW216132
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|9254230|gb|BE344698.1|BE344698
EST:     ATTTTGGCAGCATTGACATACTATTTCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31355683|gb|CD440040.1|CD440040
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|211375763|gb|FL457930.1|FL457930
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|67022814|gb|CO451563.1|CO451563
EST:     CTCTTGCTTATGGCCCAGA-                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: CTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|13150169|gb|BG320491.1|BG320491
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31353471|gb|CD437828.1|CD437828
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTCGT-GGAAACCTCAAGAAGAGGCTATCTTGCGGCAAT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTT-GTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAAT
EST: gi|7162427|gb|AW520049.1|AW520049
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|111990916|gb|EE332354.1|EE332354
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|31354494|gb|CD438851.1|CD438851
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|32908050|gb|CF012863.1|CF012863
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGCAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
EST: gi|71766309|gb|DR964246.1|DR964246
EST:     ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG                         GTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT
genomic: ATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATT

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), 48 (downstream exon)
Score: 657

GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 349

GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 178

GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 1847

GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAGgtacaatctc ... ttttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgtgacactttgtctaaccatcttaaaaaccacctatattcattttgtgaagGTAACGAAGCCTTTGTTGGAAACCTCAAGAAGAGGCTATCTTGCGGCAATTTCTGCATCCAGTTACTCCTATGTTTCATTGCTTCAGCACTTCCTTCCTA
              gtctaac  putative branch site (score: 1847)
                                         ttcatttt  putative PPT
                                     tatattcattttgt  TA-rich tract