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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgtccagtccaaaagatgatacatttcttacaccttgttttcaactaacattccaaccttttactatatacaatgaactccattttggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT

Basic information

species Zea mays
transcript GRMZM2G473001_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 9
gtctgttgtccagtc-caaaagatgatacatttc----ttacaccttgttttcaactaac-attccaaccttttactata----------tacaatgaactccattttggttt----ctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT
|| ||||  | |    |   |     |||| |||    ||  ||  |  | | ||||    ||| |  | | |||  |||          ||||||||    | ||||  |||     |||||||||||| || ||||||||||| |||||||||| ||||||||||||||||||||| || || || || ||||| ||||||||||| |||||||| ||||
gtatgttcactaaaaacttcaaccagtacaattccaacttgtacagtactctgaactcctgattactccttgttatcatacaaaagatagtacaatgattggcttttttttttttacttcagGTTGCTGGCCATAGGGATCTTCTTGAAGGTGACCCCTACCTGAAGCAGCGGCTCCGACTCCGCGACGCCTACATAACCACCCTGAATGTCTGCCAAGCCT

upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G36670.1 (Glycine max), 3'ss of exon 10
-gtctgttgtccagtccaaaagatgatacatttcttacaccttgttttcaactaacattccaaccttttactatatacaatgaactccattttggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT
     | | |   | |    |  |  | |  | |||      || ||     ||  |||||   |       |     ||  ||     |||    ||   ||||||||||||||| |||| |||| ||||| |||| |||| |||||||  | || || || |||||  | |||||||| ||||| || || |  || ||||
ctcaaggtcttttgcctcccaactttttctctcctttatttatgcttcatgttattattccctaccaagttcaggcctaacaaatcttgttt---atttatagGTTGCTGGGCACAAGGATATTCTTGAAGGAGACCCCTACTTGAAGCAAAGACTTCGTCTTCGTGACTCATACATCACAACCCTCAATGTGTTGCAAGCCT

upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA12G33820.1 (Glycine max), 3'ss of exon 9
gtctgttgtccagtccaaaag-atgatacatttcttacaccttgttttcaactaacattccaaccttttactatatacaa-tgaactccattttggtttctca--gGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT
   ||  |  ||    | ||| ||| || ||| ||    ||||    |  | | |  |   ||   | | |    | ||     | |  || ||| ||  | |  |||||||||||||| |||| |||| ||||| |||| |||| |||||||  | || || || |||||  | |||||||| ||||| || || |  || || |
--atgaggggcaaattagaagcatgctatattgctatggcctt----ttgaatcatgtcataattctctgcctagttcaggcctaataaatcttgtttatttatagGTTGCTGGGCACAAGGATATTCTTGAAGGAGACCCCTACTTGAAGCAAAGACTTCGTCTTCGTGACTCATACATCACAACCCTCAATGTGTTGCAAGCTT

upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 9
gtctgttgtccagtccaaaagatgatacatttcttacaccttgttttcaactaacattccaaccttttactatatacaatgaactccattttggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT
       || | ||  |   ||  | ||| |  || ||    | |||| |        |   ||||||          |||| ||  || |   ||    || |||||||||| || |||||||||||||| ||||  ||| |||| ||| | ||||| || |||||||| ||||| || ||||| || || ||||| || |
-------gtactgtataggggaaaa-acagtagtt-cattggggtttccatgg-----ctggccttttga-----gtgatgatcttaatctgttttctgtagATTGCTGGGCATAGAGATCTTCTGGAAGGCGACCCATACTTGAAACAGAGACTCCGGCTTCGTGATGCATACATAACGACCCTTAATGTGTGCCAAGCAT

upper sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 9
gtctgttgtccagtccaaaagatgatacatttcttacacctt---gttttcaactaacattccaaccttttactatatacaatgaactccattttggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT
  |||  |   | | || ||  |||    ||||  || | |    ||||  || | | |     |     | | | |     |    |    | ||  ||   || ||||||| |||| ||| ||||| ||||| || | |||| |||||||  | ||||||||||||||  | |||||||| ||||| || |||||||| || |
--ctgaaga--atttcagaacctgaattgtttccaactcatgagagtttcaaaatgatagattgagtaacttcca-acttgtttttttttcctctgtattggtagATTGCTGGACACAAGGACCTTCTTGAAGGGGATCCCTACTTGAAGCAAAGACTCCGCCTGCGTGACTCCTACATCACAACCCTAAATGTCTGCCAAGCAT

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|12967882|gb|BG264829.1|BG264829
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|33466458|gb|CF243507.1|CF243507
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTTTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTTTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|60401362|gb|DN234169.1|DN234169
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|12967885|gb|BG264832.1|BG264832
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|33098536|gb|CF058496.1|CF058496
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|211185310|gb|FL189476.1|FL189476
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|32940542|gb|CF045361.1|CF045361
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|50332031|gb|CO527157.1|CO527157
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTTTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTTTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|67014093|gb|CO442842.1|CO442842
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|50332032|gb|CO527158.1|CO527158
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|32846987|gb|CD986668.1|CD986668
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|33098960|gb|CF058920.1|CF058920
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACCAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCAC-AGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCG
EST: gi|12968164|gb|BG265111.1|BG265111
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|12968178|gb|BG265125.1|BG265125
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|12968179|gb|BG265126.1|BG265126
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|33466459|gb|CF243508.1|CF243508
EST:     GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
EST: gi|32844626|gb|CD984307.1|CD984307
EST:     GTGAGAAGCTGAGGGCCACCTATGAGGAAACCCAGAAGCTTCTACTTCAG                         GTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG
genomic: GTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 261

TGCCGCACTGTATGACAAACTCCTCGTTTCAGAGGAACTGCATCCATTGGGTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 487

TGCCGCACTGTATGACAAACTCCTCGTTTCAGAGGAACTGCATCCATTGGGTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 146

TGCCGCACTGTATGACAAACTCCTCGTTTCAGAGGAACTGCATCCATTGGGTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 241

TGCCGCACTGTATGACAAACTCCTCGTTTCAGAGGAACTGCATCCATTGGGTGAGAAGCTGAGGGCCAACTATGAGGAAACCCAGAAGCTTCTACTTCAGgtctgttgtc ... ggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactaacattccaaccttttactatatacaatgaactccattttggtttctcagGTTGCTGGGCACAGGGATCTTCTGGAAGGTGACCTCTACCTGAAGCAGCGGCTCCGCCTGCGTGATGCGTACATCACCACCCTGAACGTCTGCCAGGCCT
 aactaac  putative branch site (score: 241)
                                               tttctc  putative PPT
                 ttttactatatacaat  TA-rich tract