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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatacccttttcattctcagtatagaactagagcaaatagactctcaagatatgactcgattctctctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG

Basic information

species Zea mays
transcript GRMZM2G139977_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 14
-----gtactataccc-ttttcattctcagtatagaactagagcaaatagactctcaagatatgactcgattctctc-tgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG
       |||  ||   | |||  |    ||  ||||   ||||||||||   || ||  ||| ||| ||| ||  | |  |||||||||| ||| ||||| |||||||||||||||| ||||||||||| ||  |||||||||| || ||||||||||| ||||| ||||||||||| || ||||
gtaactgactgaacttatattctcttcttgttgagaaaaggagcaaatagtaact-aacgtataacttgatccttccatactttagGTTGACATTGTTGGGTTGCCCAAAGATACCAAGGATAGAGATGATATTCTGGAAAGTGAATTTTTTGACACCAGGCAGGCCTTCCTTAGTCTCTGTCAAG

upper sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------------gtactatacccttttcat---tctcagtatagaactagagcaaat-----agactctcaagatatgactcgattctctctgtttt--agGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG
                                      |  |||    |  |||    | | |   |   |  |  ||  ||     | | ||| |  | |  | |    |  ||      |  ||||||| ||    |  || ||   |||||| || ||||  ||||| ||  |||| ||||| ||||||||||||||||||||||| || |||||||| ||||
gtaagttctataatccattagttaatatagttaatttttgttatgttttggtcaactatttgaaggttacatcaatgcttatttgcaatattctgatcagaaaattgagcttgctaaaccctgcagGTTGAAATCAACGACGTACCTTCAGATACTAAGGATAAGGATGAGATTCTGGAGAGTGAATTCTTTGACACCAGACAGGCATTTCTGAGTCTTTGTCAAG
















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|76010441|gb|DT937611.1|DT937611
EST:     ACAGGGAGAGGCACCCGAGTAATAATAGAGACACACATATGCTCCATCCG                         GTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTG
genomic: ACAGGGAGAGGCACCCGAGTAATAATAGAGACACACATATGCTCCATCCGgtactatacc ... tctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTG
EST: gi|71440180|gb|DR821230.1|DR821230
EST:     GAGACACACATATGCTCCATCCG                         GTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTG
genomic: GAGACACACATATGCTCCATCCGgtactatacc ... tctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTG

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: 165

GTGTTATGATGCAGAACAGCAACTTGACGACAGGGAGAGGCACCCGAGTAATAATAGAGACACACATATGCTCCATCCGgtactatacc ... tctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

GTGTTATGATGCAGAACAGCAACTTGACGACAGGGAGAGGCACCCGAGTAATAATAGAGACACACATATGCTCCATCCGgtactatacc ... tctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GTGTTATGATGCAGAACAGCAACTTGACGACAGGGAGAGGCACCCGAGTAATAATAGAGACACACATATGCTCCATCCGgtactatacc ... tctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 159

GTGTTATGATGCAGAACAGCAACTTGACGACAGGGAGAGGCACCCGAGTAATAATAGAGACACACATATGCTCCATCCGgtactatacc ... tctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagaactagagcaaatagactctcaagatatgactcgattctctctgttttagGTTGATATTCTTGGGGTGCCCAAAGATACCAAAGATAGAGATGACATCTTGGAAAGTGAGTTCTTTGACACCAGACAGGCATTCCTTAGTCTTTGCCAAG
                                        ttctctctgtttt  CT-rich tract
              aaataga  TA-rich tract