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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatatgtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacag

Basic information

species Zea mays
transcript GRMZM5G840582_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 8
ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactct--gttttggaacaacatatgtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacag
|||||||| ||||||||||||||||||||||| | ||| ||||| |||||||| ||||| |||||||||||  |||||    ||| ||||||  |    |  |||   || |    | || ||    ||     ||| |||    ||   ||     | |  |  |                                                                     
ACAGTAGACGAGATCTACAAGGTTGCATCAATCGCACTCAGTCCAAATGTTCCTGGGCAGATCTTTgtaagtcaaacaatattcattgtttttgtgcaattatctaaaacagctttccgttcttccagtggccaaaccacaagctttaaaactggaaatatgatat---------------------------------------------------------------------

upper sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G03260.2 (Glycine max), 5'ss of exon 10
ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatat--gtttggaccacctacaccaattgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacag
||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| ||||| ||    |     || |||||||   ||   |  | |     |  ||    ||  ||  ||   |     || |  ||  | ||   ||    |  | |   ||    | || ||  | |   |||||    |  | ||                            
ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTTgtgagtttgat----ctaaatgtttc--tcagatattttaat-ttagacttaatatacttgttcaaagtgttattttagtgagtactttctctttccttgggaatttcctcattattcatatttcttaccctgttctacag----------------------------

upper sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G04320.2 (Glycine max), 5'ss of exon 10
ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaacacggctcaatgttttattcttttgctcttccactgaacccggtactctgttttggaacaacatatgtttgg--accacctacaccaattgttc-ttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacag
||||| |||||||||||||||||||||||||||  ||| ||||| |||||||| |  ||||| ||||| ||    |     || |||||||   ||   |  | |     |  ||    ||  |   ||   |     || ||  ||   ||      |     |||  | ||    | || ||  | |   |||||    |  | ||                            
ACAGTTGATGAGATCTACAAGGTTGCATCAATATCACTTAGTCCAAATGTTCCAGCACAAATATTTgtgagttggat----ctgaatgtttc--tcagatattttaat-ttagacttaatatacctgttcaaagtgttatttgagtgagtactgttctctttccttgggcatttcctcattattcatatttcttaccctgttctacag----------------------------

upper sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 5'ss of exon 10
ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaacacggctcaatgttttattcttttgctct---tccactgaacccggtactctgttttggaacaacatatgtttggaccacctacaccaat-tgttcttaaagctttgtttctttgctttaccaaactacagagcgtagttgcttaagtctgccttttacag
|| || |||||||| || |||||||||||||||  ||| ||||| ||||| || ||||| || ||||||||    |    |   ||| ||||||| | | ||  |   | || |||||  | ||||||  |||       | | ||||   ||||      |  |  | |  ||  |  |||  |||||| ||||  ||                                      
ACTGTTGATGAGATTTATAAGGTTGCATCAATATCACTCAGTCCAAATGTCCCTGGGCAGATATTTgtaagttgga----gtctaatattttattttgtggcattctgttcattgaactggatactctcattt-------cctctgttcataccattatttctgagatatgttttcatattttcttctttccttttacag-------------------------------------

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|32942724|gb|CF047543.1|CF047543
EST:     ACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|78112475|gb|DV530869.1|DV530869
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|32850940|gb|CD990621.1|CD990621
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|32807630|gb|CD959864.1|CD959864
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTA
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTA
EST: gi|91054117|gb|EB164535.1|EB164535
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|7216933|gb|AW563070.1|AW563070
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATAC
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATAC
EST: gi|32845230|gb|CD984911.1|CD984911
EST:     TACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: TACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
EST: gi|7227753|gb|AW566394.1|AW566394
EST:     ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTT                         ATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG
genomic: ACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAG

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), 48 (downstream exon)
Score: 36

ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG


Block sizes: 36 (upstream exon), 45 (downstream exon)
Score: 7

ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 31

ACAGTAGATGAGATCTACAAGGTTGCATCAATAGTACTGAGTCCGAATGTTCCCGGGCAAATCTTTgtaagcgaaa ... ccttttacagATGGGAGTGATGGTTAACCCTCCTAAACCTGGAGATATCTCATACCCGAAGTTCACTGCCGAAAG