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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagtcgccaatcatttttccatatgtatagctgcctaggttctatgcttgctagaagaaaatgctgaagatacaactgcagtgtgttacctgtttctcataaaagctttagagctgacaataacattgagctttcttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG

Basic information

species Zea mays
transcript GRMZM2G070422_T02
intron # 6
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 6
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 6
gtatgcagtcgccaatcattt--ttccatatgtatagctgcctaggttctatgcttgctagaagaaaatgctgaagatacaactgcagtg--tgttacctgtttctcataaaagctttagagctgacaataacattgagctttcttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG
|| || ||  || |  |||||  |||||||||| || |    |    |   ||  ||    || | ||   |         | | || |   | | |   | || |  |  ||||||| |||||   | |||  |    || | || |||| | ||||||||| ||| ||||| | |||||| |||||||||||||||||  | ||||||||||| |||||||| ||||||
gtgtgtagatgcaatccatttcattccatatgtctacccagttgatatacttgggtgtgcaaaaacaacattaggcgcgtta-tacaatttctataattggattgttttttaagcttttgagctttgactaaactactcctatttttatttgatagGAAGTTGCTGAGTCAGTCAAGAATGACTTTGGCAGCATTGACATTTTGGTGCATTCTCTAGCTAATGGTCCAGAG

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 5
gtatgcagtcgccaatcatttttccatatgtatagctgcctaggttctatgcttgctagaagaaaatgctgaagatacaactgcagtgtgttacctgtttctcataaaagctttagagctgacaataacattgagctttcttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG
                                          | | |  || ||  ||| |   | |     |  |    || |||| |||     |||    | |  |||| ||   || |   ||   |     ||  || | || | ||||||||| |||||| || | ||| ||||||||||  || |||||||| ||||| || ||||||||||| ||||||
-----------------------------------------ggatgcattgtttagtagcatttactttgtgatctgtgtct-cagtttgt-----gttgtaaagactagctgta---ctcagtctactgt--gatttgttttacttcatagGAAGTTGCTGAATCTGTCAAGAAAGATTTTGGCACTATCGACATACTTGTGCACTCGCTTGCTAATGGACCAGAG

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 6
gtatgcagtcgccaatcatttttccatatgtatagctgcctaggttctatgcttgctagaagaaaatgctgaagatacaactgcagtgtgttacctgtttctcataaaagctttagagctgacaataac------attgagcttt-cttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG
                                                          | |   | || | | | | ||  | |  |||| |   ||| ||   |      || |   ||  |  ||        | || | |||  || |  | | ||||||||| |||||| || | ||| ||||||||||  || |||||||| ||||| || ||||||||||| ||||||
----------------------------------------------------------ggatgcattgttta-gttgcatttactttgtgatctgtgtctcagtttgtgttttaaagactagctgtactcagtctactgtgatttgttttaccttatagGAAGTTGCTGAATCTGTCAAGAAGGATTTTGGCACTATCGACATACTTGTGCACTCGCTTGCTAATGGACCAGAG

upper sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcagtcgccaatcatttttccatatgtatagctgcctaggttctatgcttgctagaagaaaatgctgaagatacaactgcagtgtgttacctgtttctcataaaagctttagagctgacaataacattgagctttcttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG
                                                        ||||  | |       | | ||  |||||   |   |  |||| ||| | || |||||                |||   || |||||   | ||||||| || |||||  ||||  || |||||||| ||||||||||| || || ||||| ||||| ||||||||||||
-----------------------------------------------------gtatagattagagatacacaaacacgcctgcaagttaacatgtgttactccttaatgcttt----------------ttg---ttgcttaa---atcagGAAGCTGCTGAATGTGTGAAAAAAGATTTTGGAAGCATTGACATTCTTGTCCATTCCCTTGCAAATGGCCCAGAG

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:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|211267881|gb|FL003946.1|FL003946
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|31361470|gb|CD445827.1|CD445827
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|32914780|gb|CF019592.1|CF019592
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|67017641|gb|CO446390.1|CO446390
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|31356384|gb|CD440741.1|CD440741
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|67019739|gb|CO448488.1|CO448488
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|31357208|gb|CD441565.1|CD441565
EST:     GATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|24774150|gb|CA409404.1|CA409404
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACT
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACT
EST: gi|31362224|gb|CD446581.1|CD446581
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|67042246|gb|CO468501.1|CO468501
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|84980240|gb|DW530589.1|DW530589
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|6526869|gb|AW216132.1|AW216132
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGNTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|6022101|gb|AW067029.1|AW067029
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCA
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCA
EST: gi|9254230|gb|BE344698.1|BE344698
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTATTT
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|31355683|gb|CD440040.1|CD440040
EST:     GTCTTTTTTAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|211391003|gb|FL321745.1|FL321745
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGCCAGTAAAAG                         GAAGTTGTTGAATCAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAA-Ggtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTG
EST: gi|211021063|gb|FL329760.1|FL329760
EST:     GTCAAATCGAACAAA-GATATGCAGGGGCATCAAACTGGACAGTAAAA                         GAAGTTGT-GAATCAGTGAGGAATGATTT
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTT
EST: gi|24774154|gb|CA409408.1|CA409408
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTA
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTA
EST: gi|13150169|gb|BG320491.1|BG320491
EST:     ATGTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: ATGTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|211135434|gb|FL356365.1|FL356365
EST:     GTCAAATCGAACAAAAGATATGCANGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAA
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAA
EST: gi|31353471|gb|CD437828.1|CD437828
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|7162427|gb|AW520049.1|AW520049
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|111990916|gb|EE332354.1|EE332354
EST:     TATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: TATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|211164083|gb|FL357846.1|FL357846
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTG
EST: gi|24774062|gb|CA409316.1|CA409316
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|31354494|gb|CD438851.1|CD438851
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|32908050|gb|CF012863.1|CF012863
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|78023662|gb|DV492049.1|DV492049
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|211267880|gb|FL003945.1|FL003945
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
EST: gi|88751885|gb|DY536026.1|DY536026
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAATCTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGT
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGT
EST: gi|71766309|gb|DR964246.1|DR964246
EST:     GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAG                         GAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG
genomic: GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTG

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: 513

GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 364

GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1410

GTCAAATCGAACAAAAGATATGCAGGGGCATCAAACTGGACAGTAAAGgtatgcagtc ... aatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcataaaagctttagagctgacaataacattgagctttcttaatttaacagGAAGTTGTTGAATCAGTGAGGAATGATTTTGGCAGCATTGACATACTAGTGCATTCTCTTGCTAATGGCCCAGAG
                                      ctttctta  CT-rich tract
                                       tttcttaatttaaca  TA-rich tract