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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcaatgtcatggtaattattgtagtatcaagtcaggtttagcatagaaacataacctttctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA

Basic information

species Zea mays
transcript GRMZM2G141587_T05
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 17
gtgctcaatgtcatggtaattattgtagtat-caagtcaggt-ttagcatagaaacataacctttctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA
|||| |  |||  || ||||||||||| | | ||| |||||  | || ||   || |||||| || | ||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||||||||| ||| ||||||||||||||||| |||| ||||| |||||||| 
gtgccccctgttctgctaattattgtactctgcaactcaggcctcagaatctgaagataacccttttatttgcagTGTGGCACGTTTCTTGGAATCACGGGGCATGTTGGAAGAAGCCCTTGAGATAGCAACAGACTCTAATTACAGATTTGACTTGGCCGTGCAGCTTGGTCGG

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 8
gtgctcaatgtcatggtaattattgtagtat-caagtcaggt-ttagcatagaaacataacctttctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA
|||| |  |||  || ||||||||||| | | ||| |||||  | || ||   || |||||| || | ||| ||||||||| |||||||||||||||| ||| |||||||| |||||||| ||||||||||| ||| ||||||||||||||||| |||| ||||| |||||||| 
gtgccccctgttctgctaattattgtactctgcaactcaggcctcagaatctgaagataacccttttattttcagTGTGGCACGTTTCTTGGAATCACAGGGCATGTTGGAAGAAGCCCTTGAGATAGCAACAGACTCTAATTACAGATTTGACTTGGCCGTGCAGCTTGGTCGG

upper sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
--------------------gtgctcaatgtcatggt-aattattgtagtatcaagtcaggtt-tagcat----agaaacataacctttctttttgc-agTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA
                    |      |    | | | ||||||| |    ||   | || || | ||||    | ||  | |    ||    |||| |||||||| |||||||||||||||||||| ||| | ||||| ||||| ||  |||| |||||| || ||||| ||||||| || ||  |||| |||||  ||
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA

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|22489660|gb|BU049570.1|BU049570
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|18963894|gb|BM660690.1|BM660690
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|67013287|gb|CO442036.1|CO442036
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|18384433|gb|BM417632.1|BM417632
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|18649807|gb|BM498626.1|BM498626
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|211291668|gb|FL235608.1|FL235608
EST:     GATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCACGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|21809537|gb|BQ667855.1|BQ667855
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|89106141|gb|DY576358.1|DY576358
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|18649903|gb|BM498722.1|BM498722
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|18649808|gb|BM498627.1|BM498627
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGACCAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
EST: gi|18384334|gb|BM417533.1|BM417533
EST:     GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGAT

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), 49 (downstream exon)
Score: 301

TACTCCTTAGTTTGATCGAATATAAAACACTTGTAATGCGTGGGGATTTCGATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 450

TACTCCTTAGTTTGATCGAATATAAAACACTTGTAATGCGTGGGGATTTCGATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

TACTCCTTAGTTTGATCGAATATAAAACACTTGTAATGCGTGGGGATTTCGATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 803

TACTCCTTAGTTTGATCGAATATAAAACACTTGTAATGCGTGGGGATTTCGATCGCGCGAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctcaatg ... ctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attattgtagtatcaagtcaggtttagcatagaaacataacctttctttttgcagTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA
                                  acataac  putative branch site (score: 803)
                                        cctttctttttgc  CT-rich tract
                                          tttcttttt  TA-rich tract