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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtagtttgtgtatgaaattgaaatctagtaatatacacttttgaaccaaaagttgttagttctaagctctgttacaaattctttctgtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG

Basic information

species Zea mays
transcript GRMZM2G019361_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019361_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 11
gtgtagtttgtgtatgaaattgaaatctagtaatatacacttttgaaccaaaagttgttagttctaagctctgttacaaattc-tttctgta-tttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG
              |  | || |  |  |||    |||| |||| | |  ||     | | | | |    |||   ||| ||  |||||||  ||||||||| ||||||||  ||||||| |||||||||||||| ||||||||||||||||||||| |||| |||
-------------gtacagtt-atttacagtg-cgtacattttttaccagaagacaatgaatccca----ctgcctcaacttgatttctgtgctttttagGTTAATCAAATTAGAGATTCTTTGGCAGTTATGGGCAACAACAGCACTGCTTTTAGCCTGCCCCAG

upper sequence: GRMZM2G019361_T03 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G16130.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------gtgtagtttgtgtatgaaattgaaatctagtaatatacacttttgaacca-----aaagttgttagttctaagctctgttacaaattctt-----tctgtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG
                                                              | | |   | ||  |||  | |||  ||| || || |||  ||  |     | | | ||    |||    | ||||  | |    |     ||    |  | ||||||||||||| || ||||| |||||  |||||||  ||||||||||||| |||||||| || || 
gtttgttttaaagcatatgatctgatggaaggctttgtttactatttaatgcagggaacaaaaatattgatgtggtatttta-tcttctaaaattcaatttccaattatcagtagaatagtacagtctggaatatgttttataacactaaaagtcaacttcatcagGTCAATCAAATCCGGGATTCATTGGCTATTATGGGTGACAACAGCACTGCCTTTAGCTTACCGCAA

upper sequence: GRMZM2G019361_T03 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------------------------------------------gtgtagtttgtgtatgaaattgaaatctagtaatatacacttttgaaccaaaagttgttagttc--taagctctgttacaaattctttctgtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG
                                                                                       ||| ||| | |   ||| |  ||| |   | ||| || |     |  |  |||    | ||   || | | | | |||       ||    |  | ||||||||||||| |||||||| ||||| ||||||||  ||||||| ||||| |||||||| || || 
gtatggttttccatttgttttaaagcaaatgatctgatggaaggctttgtttactatttaattgcagggaacaaaaatattgatatggtattttatcttctaaaattcaatttccgattat-cagtaaaatagtactagtctggaattgaatatgttttataacactaaaagtcaacttcgtcagGTCAATCAAATCCGAGATTCATTGGCTGTTATGGGTGACAACAGTACTGCCTTTAGCTTACCGCAA

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|31361636|gb|CD445993.1|CD445993
EST:     TAATGGTGACAAATATATTGATGAG                         GTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCT
genomic: TAATGGTGACAAATATATTGATGAGgtgtagtttg ... gtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCT
EST: gi|91050205|gb|EB160623.1|EB160623
EST:     TAATGGTGACAAATATATTGATGAG                         GTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCT
genomic: TAATGGTGACAAATATATTGATGAGgtgtagtttg ... gtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCT

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: 20 (upstream exon), 49 (downstream exon)
Score: 172

GTGACAAATATATTGATGAGgtgtagtttg ... gtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 101

GTGACAAATATATTGATGAGgtgtagtttg ... gtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 110

GTGACAAATATATTGATGAGgtgtagtttg ... gtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 112

GTGACAAATATATTGATGAGgtgtagtttg ... gtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaccaaaagttgttagttctaagctctgttacaaattctttctgtatttttagGTCAATCAAATACGAGATTCGTTGGCAGTTATGGGGAACAACAGCACTGCTTTTAGCTTGCCTCAG
                                     ttctttctgtattttt  CT-rich tract
                                        tttctgtattttta  TA-rich tract