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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagttccttctgtttgttttctatcatttttaatattaatagattgcattttctgctaatttggaattttaattcactatttcttgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
gtactagttccttctgtt--tgttttctatcatttttaatattaatagattgcattttctgctaa-tttggaattttaattcactatttcttgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG
||| |  || || |   |  | | || ||  || |||  ||     |  |    || | |||||| | ||| |       |   | |   |  | || ||||||||||||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||| ||||| |||
gtaatgttttctccaaatgctatcttgtaggatgtttgttagc--caagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
---------------gtactagttccttctgtttgttttct---atcatttttaatattaatagattgcattttctgctaattt-----ggaatttta--attcactatttcttg-tcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG
               |   | |    |  ||||||  |  |   |  | || ||||  |   |||| |  |  | || |    |     || || |||  |||  || ||  | | | || |||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| |||||||||||||||||  ||
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagat-gtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
---------------gtactagttccttctgtttgttt---tctatcatttttaatattaatagattgcattttctgctaat-ttggaattttaattcactatttcttg-----tcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG
               |     | |  |  ||||||  |   | ||  | || ||||  |   |||| |  |  | || |    ||||  | |    | |   | | |||     | || |||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| || |||||||| |||||||||||||||||  ||
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagat-gtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtactagttccttctgtttgttttctatcatttttaatattaatagattgcattttctgctaatttggaattttaattcactatttcttgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG-------------
    || |||||  | |   | |  | | || ||| || | |||      |||||| |  |   ||| |                       || ||||||||||||||||| |||||||||||||| || |||||||||||    ||||| |||||||||||||| |||||||||  |||| ||             
---gtaattcctcttttacttctcttcttatctttcatctcaatg---ctcattttgtatttgcttgca----------------------tttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtactagttccttctgtttgt--tttctatcatttttaatatta-atagattgcattttctgctaatttggaattttaattcac--tatttcttgtctt-acagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG
   ||| | |         || |  |||| |||  | ||| || || |||   | |  | |||     | ||    | | | |||   ||||  || ||||  ||||| ||||||||||| ||||||||||||||||||||||| |||||    || || ||||| || ||||||||||| ||||| || |||
gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG

upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtactagttccttctgtttg-----ttttctatcatttttaatattaatagattgcattttctgctaatttggaattttaattcactatttcttgtc--ttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG
                        || ||  ||  |  ||     ||||||    |   ||||  ||  ||  |     || || |   |   |||||       || ||   || |  || ||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || || || ||||||||||| || || ||  ||
gtaggcaacagaatacctcccctgtattttgttaaggctgaagctttttctcaggtccataatcataccagtgtatcgcttttgttgcatgacaatttatgccttcttttctatgccacttgcagCTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAG

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|71306846|gb|DR789579.1|DR789579
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211448759|gb|FL324438.1|FL324438
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|60352104|gb|DN219077.1|DN219077
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|148951738|gb|EC897493.2|EC897493
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|149100779|gb|EE186873.2|EE186873
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|148950117|gb|EC895653.2|EC895653
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|71310911|gb|DR791758.1|DR791758
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211504975|gb|FL314285.1|FL314285
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|148964886|gb|EE015748.2|EE015748
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|78117582|gb|DV535969.1|DV535969
EST:     GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA

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: 46 (upstream exon), 47 (downstream exon)
Score: 157

GCTATCTGTTGTCGATAGCTACAAGATTTTGAAGGGTGTTGACGTTCTGAGCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 741

GCTATCTGTTGTCGATAGCTACAAGATTTTGAAGGGTGTTGACGTTCTGAGCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 742

GCTATCTGTTGTCGATAGCTACAAGATTTTGAAGGGTGTTGACGTTCTGAGCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 230

GCTATCTGTTGTCGATAGCTACAAGATTTTGAAGGGTGTTGACGTTCTGAGCAAGGAGGAGACATTTCTGGCCTGCACCCTTGGCTGGTGTATTGAATGGgtactagttc ... tgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagattgcattttctgctaatttggaattttaattcactatttcttgtcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG
                                     ctatttcttgtctt  CT-rich tract
                         aattttaattcactat  TA-rich tract