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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacataaggccggtgacatgctaagctttatttagttggtattttccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG

Basic information

species Zea mays
transcript GRMZM2G120178_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g05710.1 (Oryza sativa), 3'ss of exon 3
------------------------gtaacataaggccggtgacatgcta--agctttatttagttggtatttt-ccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
                         ||     |     |||    | |   |||||  ||   |||  ||||  |||| |||||  ||| ||||||   ||  | ||  |||| |||  ||||||||||| ||  | ||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||| ||||||||||||
gtaatgtttgatttcttcttattgctattgagatattcgtgtttggttggcagcttacttgcattgccatttaaccttctcatggtttgggccttacaatagttattttaaacaaatggcagAAACAATCTGAACTTCTGCTTAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGCGTTATTGATGATGCTACAGGTGCTGAAAAG

upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G38000.1 (Glycine max), 3'ss of exon 3
gtaacataaggccggtgacatgctaagctttatttagttggtattttccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
              ||  |||  |  |||||| ||  ||| |  ||        |    || |   || |   | | |        |||   ||||||||||| ||  |  ||||||||||||||||| | ||||| |||||||| ||  | ||||| || || || || ||||||||||||||||| ||||||
--------------gtatcattttccgctttacttctttgttgcttaa------acagtttatattttctca-accctggtgtgttcaa---cagAAACAATCCGATCTTTTGCTGAATGCTGATGATTTGGATGCAATGTGGGTGTGCTTAAGAGAGAACTGCGTCATTGATGATGCTACTGGTGCAGAAAAG

upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G02700.1 (Glycine max), 3'ss of exon 2
gtaacataaggccggtgacatgctaagctttatttagttggtattttccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
                             | ||||  | ||  |  |   ||  |    || |   || |   ||   | |       |  |||||||||||| ||  |  ||||||||||||||||| | ||||| |||||| | ||  | ||||| || || || || ||||||||||||||||| ||||||
------------------------gtatatcattt--tcggcttcgttgcttaaacattttatatattttctcattcctgccgtgttca--acagAAACAATCCGATCTTTTGCTGAATGCTGATGATTTAGATGCAATGTGGATCTGCTTAAGAGAGAACTGCGTCATTGATGATGCTACTGGTGCAGAAAAG

upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G18580.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaacataaggccggtgacatgctaagctttatttagttggtattttccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
          |    |  | ||||     ||||| ||  |   |||    |||      |||  |  |  | ||| ||    ||  |    |||||||||||| ||  |  || | || ||||||||| | | ||| |||||||||||| | |||||||||||||| || |||||||| |||||||||||||||
----------gtatttcgcctgctcttaattattcagaagaagtttaatgttt------ttgctcacttcgatatgttgattaattc--ccacagAAACAATCGGATCTTTTGTTAAACGCTGATGATTTGGCTGCTATGTGGGTTTGTTTGAGAGAAAATTGTGTGATTGATGATGCCACTGGTGCTGAAAAG

upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv05s0020g01710.t01 (Vitis vinifera), 3'ss of exon 3
--------gtaacataaggccggtgacatgctaagctttatttagttggtat--tttccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
         |  ||||  |  | |||     | | | ||   | ||| || |  |||  |||| |     | || || | | ||| | |||     |   | ||||||||||| ||  |  |  | |||||||||||| | ||||| |||||||||||  | |||||||||||||| || |||||||| ||   ||||||||||
caatatggttgccatagtgtagttgatcatttgaccatttgattgttagtttaatttggttttaacagtatctgactcaagttatatcttc-----cttgtgcagAAACAATCTGATCTTTTATTAAATGCTGATGATTTAGATGCAATGTGGGTTTGCTTAAGAGAAAATTGTGTGATTGATGATGCCACAAATGCTGAAAAG

upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ29777 (Selaginella moellendorffii), 3'ss of exon 3
gtaacataaggccggtgacatgctaagctttatttagttggtattttccttttcatgacttgtgcctta---tggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
                           ||||     |||  |  |||| | || | || || | |  |    ||||||  |||    |    || ||||| ||| ||||||||||| | |||||||||||||| |||||  ||||||||||| |  | || || ||||| || || ||| | |||||  ||||||||
-------------------------gtctttgaaaggtttttgatttcatcttgaggattttttctctgaagtggtattgttttttgaggtgtt-cagAAGCAAGCAGAGATGCTGTTAAATGCTGATGATCTCGATGCTCTGTGGGTTTGTTTACGCGAGAACTGTGTCATTGACGATTCCACTGGAACTGAAAAG

upper sequence: GRMZM2G120178_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ08923 (Selaginella moellendorffii), 3'ss of exon 3
gtaacataaggccggtgacatgctaagctttatttagttggtattttccttttcatgacttgtgcctta---tggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
                           ||||     |||  |  ||||   || | || || |    |    |||| |  |||    |       ||||| ||| ||||||||||| | |||||||||||||| |||||  ||||||||||| |  | || || ||||| || || ||| | |||||  ||||||||
-------------------------gtctttgaaaggtttttgatttcagcttgaggattttttttctgaagtggtgttgttttttgaggtgcc-cagAAGCAAGCAGAGATGCTGTTAAATGCTGATGATCTCGATGCTCTGTGGGTTTGTTTACGTGAGAACTGTGTCATTGACGATTCCACTGGAACTGAAAAG

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|22819572|gb|BU499662.1|BU499662
EST:     GATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAG                         AAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTT
genomic: GATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAGgtaacataag ... ccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTT
EST: gi|26559863|gb|CA832098.1|CA832098
EST:     GATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAG                         AAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTT
genomic: GATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAGgtaacataag ... ccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTT

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: 295

AAACCTGAAGAAGGATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAGgtaacataag ... ccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 109

AAACCTGAAGAAGGATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAGgtaacataag ... ccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

AAACCTGAAGAAGGATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAGgtaacataag ... ccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 126

AAACCTGAAGAAGGATCTATTAGCTCTAGAGTTCAAAGGTTGGCCAAGTATAGGTTTTTAAAGgtaacataag ... ccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttccttttcatgacttgtgccttatggtatcttttcaaaaccaattacagAAACAATCAGAGATGCTGCTGAATGCTGATGATCTTGATGCCATGTGGGTTTGTCTCAGAGAAAATTGTGTAATCGATGATGCTACTGGTGCTGAAAAG
                                    ttttcaaaa  TA-rich tract