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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacttacttctgtgttgctttcaagcattttttatgttaacagaatgaattttctgctaatatgaaattttaaatcactatttcttatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
gtactacttacttctg-tgttgctttcaagcattttttatgttaacagaatgaattt-tctgctaa-tatgaaattttaaatcactatttcttatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG
||| |  || || |   || |   ||  || || |||   |||| |  | |||| || | |||||| | ||  |      ||   | |   | || |||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||| |||||||||||||| ||||| |||
gtaatgttttctccaaatgctatcttgtaggatgttt---gttagccaagtgaagttatatgctaagtgtggcaccactgatggttctgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
-----------------gtactacttacttctgtgttgctttcaagcattttttatgttaacagaa--tgaattttctgctaatatgaaattttaaatcactatttctta-----tcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG
                  |    ||| ||| | ||     || ||  | || | ||  |  ||||   | | | |  ||  | |  |     |   || | | | | ||      | ||||||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| ||||| || || |||||||||||||||||  ||
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G01820.3 (Glycine max), 3'ss of exon 3
----------gtactacttacttctgtgttgctttcaagcatttttta-tgttaacagaatgaattttctgctaatatgaaatt------ttaaatcactatttctta-----tcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG
            |   ||||    | | ||| ||  | |  | |  || |  |||  |  | |  | | | ||   |||  |||      |   || |   | | ||      | ||||||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| || ||||| || |||||||||||||||||  ||
gtatggaagttgaaagcttatgcttttcttgtttgaatgattatactagttctaatcgtttcagatgtttactgtgatggcattggggtatcttatgatcgtcttttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGCGGCCAGCCATGCTGGTTTAGAGTGCCCAAG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtactacttacttctgtgttgctttcaagcattttttatgttaacagaatgaattttctgctaatatgaaattttaaatcactatttcttat-cttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG-------------
                            | | ||  | | |||      |    ||     | || | ||   | |  |     || |||    |||||||||||||||||||| |||||||||||||| || |||||||||||    ||||| |||||||| ||||| |||||||||  |||| ||             
----------------------------gtaattcctcttttacttctctt--cttatctttcatctcaatgctcattttgtatttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtactacttacttctgtgt-tgctttcaagcattttttatgtta-acagaatgaattttctgctaatatgaaattttaaatcac--tatttcttatctt-gcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG
   ||| | | |        | | ||||||| |  | ||  |  || | |   |    | |||     ||||    | | | |||   ||||  ||||||| |||||| ||||||||||| ||||||||||||||||||||||| |||||    || || ||||| |||||||||||||| ||||| || |||
gtataccaatgataaagacttatcctttcaatctctattagtaatagatactctcctctctctctctttatgtcgctatcactcatcatattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG

upper sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------gtactac-ttacttctgtgttgctttcaagcattttttatgttaacagaatgaattttctgctaatatgaaattttaaatcactatttct---tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG
                       ||| |   |||   |||      ||||     |   | ||  || |||  |     || || |   |||| | ||||   |    |||||      ||||||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || || |||||||||||||| || || ||  ||
gtaggcaacagaatacctcccctgtattttgttaaggctgaagctttttctcaggtccataatcataccagtgtatcgcttttgttg-catgacaatttatgccttcttttctatgccacttgcagCTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAG

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|211272079|gb|FL317340.1|FL317340
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|148972761|gb|EE023734.2|EE023734
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|149102315|gb|EE188183.2|EE188183
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|149081093|gb|EE170194.2|EE170194
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211528502|gb|FL328860.1|FL328860
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGACTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|148986685|gb|EE030467.2|EE030467
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211537181|gb|FL316595.1|FL316595
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|71437045|gb|DR818095.1|DR818095
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211507953|gb|FL346110.1|FL346110
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         N
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcag-
EST: gi|211507953|gb|FL346110.1|FL346110
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         N
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcag-
EST: gi|211302622|gb|FL366315.1|FL366315
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACA
EST: gi|211278408|gb|FL366607.1|FL366607
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|18659682|gb|BM500468.1|BM500468
EST:     GCAAGGAGGAGACATTTCTTGCTTGCAACCTTGGNTGGTGCATTGAATGG                         NTTCAAGCTTATTTTCTTGTGNTTGATGATAT
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATAT
EST: gi|211268113|gb|FL358780.1|FL358780
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCC-AGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211222998|gb|FL350874.1|FL350874
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211226829|gb|FL341085.1|FL341085
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTC
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTC
EST: gi|148942982|gb|EC888030.2|EC888030
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211056216|gb|FL359449.1|FL359449
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|148943253|gb|EC888314.2|EC888314
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|74235474|gb|DT643388.1|DT643388
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
EST: gi|211274552|gb|FL349465.1|FL349465
EST:     GCAANGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCA
EST: gi|211460036|gb|FL333652.1|FL333652
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGGAC
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAG-AC
EST: gi|211049850|gb|FL341779.1|FL341779
EST:     GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGG                         CTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA
genomic: GCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACA

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: 102

GCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 247

GCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 248

GCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GCTCTCTGTCATTGATAGCTACAGGATATTGAAGGGTGTTGATGTTCTGAGCAAGGAGGAGACATTTCTTGCTTGCACCCTTGGCTGGTGCATTGAATGGgtactactta ... tatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaatgaattttctgctaatatgaaattttaaatcactatttcttatcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG
              tgctaat  putative branch site (score: 197)
                                     ctatttcttatctt  putative PPT
                 taatatgaaattttaa  TA-rich tract