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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatttacctctcttgtttcacttattgatccttttgttgagttgatggatttgcatcgatggttctatgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 6
gtaagaaatttacctctcttgtt-tcacttattgatccttttgttgagttgatggatttgcatcgatggttctatgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
||||| ||  ||| |   |  ||   |  | ||||  ||||  ||||||||||||||||||||  |||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||||
gtaagcaaactactttcgtcattgctaagtcttgactcttt-attgagttgatggatttgcatgaatggttctatgcctgcagCTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaagaaatttacctctcttgtttcacttattgatccttttgttgagttgatggatttgcatcgatggttctatgcct-gcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
                                 ||   | ||            | |    ||||| |  |       |   ||     ||| ||   |||||  || | | ||||||||||||| |||||||| ||||||||||||| ||||||||||||||| 
gtaagggttctttctgattctctttcattattggttgtagatgctaaaagagaatgttgtatattggttgtagatgctaaaagagaatgttgtataagtggtttcattctttgcagTTGTGTGCAGATACGGAATTGGTTTGACTATCTTAATCATATTTGTATT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 4
gtaagaaatttacctctcttgtttcacttattgatccttttgttgagttgatggatttgcatcgatggttctatgcct-gcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
|||||   | |   |   |   ||   |||||| |  |       |   ||     | | ||   |||||  || | | |||||||||||||||||||||| ||||||||||||||||||||||||||||| 
gtaagggttctttttggttgtctttctttattggttgtagatgctaaaagagattgtggtataagtggtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 6
gtaagaaatttacctctcttgtttcacttattgatccttttgttgagttgatggatttg-catcgatggttctatgcct-gcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
|||||||  || | |  ||  |   | || ||      ||| |    ||  |  |||||  ||      ||| || ||| |||||||||||||||||||||| ||||||||||||||||||||||||||||| 
gtaagaatatttctttcctcttactatttcttcgctagttt-taattttattacatttggtataagcttttcaattccttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaaatttacctctcttgtttcacttattgatccttttgttgagttgatggattt----gcatcgatggttctatgcct-gcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
||| | | | |   |||||| | |    | ||  |  || |      |||| |  |||    | ||   | |||  || | | |||||||||||||||||||||| ||||||||||||||||||||||||||||| 
gtacggactctctgtctctt-tgtgttctgttcttggttgtagaagtttgaagtgttttttggtataagtcgtttcattctttgcagTTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATTTGTATT

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|32866970|gb|CF006652.1|CF006652
EST:     GAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
genomic: GAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
EST: gi|149089547|gb|EE178794.2|EE178794
EST:     GAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
genomic: GAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
EST: gi|6095292|gb|AW119959.1|AW119959
EST:     GAAATTGATGTGCTCCAGAAACTTGGGAAGCATGACTTTACTGGCAGCCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
genomic: GAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
EST: gi|6695913|gb|AW289021.1|AW289021
EST:     GCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
genomic: GCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA

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: 117

CTATCAAGATTGTACGCTCCCTTCAGAAATACCGAGAGGCTGCTATGATAGAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

CTATCAAGATTGTACGCTCCCTTCAGAAATACCGAGAGGCTGCTATGATAGAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

CTATCAAGATTGTACGCTCCCTTCAGAAATACCGAGAGGCTGCTATGATAGAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 156

CTATCAAGATTGTACGCTCCCTTCAGAAATACCGAGAGGCTGCTATGATAGAAATTGATGTGCTCCAGAGACTTGGGAAGCATGACTTTACTGGCAGCCGgtaagaaatt ... atgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgatccttttgttgagttgatggatttgcatcgatggttctatgcctgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATTTGTATA
          ttttgtt  TA-rich tract