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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttctgtacctgttgagcaaacaaaatgggccagagaaatctgtcgaagtagtttatctaactgttcttaacttccag

Basic information

species Zea mays
transcript GRMZM2G136803_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 14
GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttctgtacctgttgagcaaacaaaatgggccagagaaatctgtcgaagtagtttatctaactgttc------ttaacttccag
||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||| |||||||||||||||| ||||| ||  |||| ||||||||| ||||||| | ||||| | ||||| ||| | | |     |  |||       ||||||||| ||| ||       || | || |||
GATAGACCATATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCAGCCACAGGTCTAGTTGGGAAATTTAGGCCTTCAATTGCTCTCAGTCAGgttggtttctgcagctgttaaacaaactaaaagagactagagagcctga------agtttatctgactttttcctatgttgattttcag

upper sequence: GRMZM2G136803_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 15
GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttctgtacctgttgagcaaacaaaa---tgggccagagaaatctgtc--gaagtagtttatctaactgttcttaacttccag------------------------------------------
||| || ||||| ||||| |||||  | || ||||| ||||| ||||||||||| |||||| | ||||| |||||  |||| || || ||||||||||||||    |  ||| | | |  |   ||        ||   ||| |||||  |||  ||| |  | || ||| |      ||  ||                                              
GATTGATCACATTTTGGGATTCTTCCGAATTTGGGAACTTCCGGATCATGCTGCGACAGGTCTTGTTGGAAAATTCCGACCATCTATTCCTCTTAGTCAGgtatactcttgttcttttaaatttaaagggcacttgatgcagtgaaatgcgtcctgaaatgctctaactagcaaaatatattttttttgtacttttagtcaatttatatttcatgtcttatctgttgtag

upper sequence: GRMZM2G136803_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 5'ss of exon 13
GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgt----------tagttt-----------ctgtacctgttgagcaaacaaaatgggccagagaaatctgtcgaagtagtttatctaa--ctgttcttaa-cttccag---------------------------------
 || || || ||  ||||||||||||| || |||||||||||||| ||||||   |||||| ||||||| || ||  |||| || |||||||| ||||||||           ||  |            |  |  |  |   |||| ||   |||| ||||   | |        || | || |||  |  ||| |   |||  ||                                 
AATTGATCATATACTGGGTTTCTTTAGAATCTGGGAGCTTCCAGAGCATGCTATGACAGGTCTAGTTGGAAAGTTCCGACCATCTATCCCTCTAAGTCAGgtactgccatgccagcctaatacaaatagttagattttctatacaaaaaatgagggcaagagtggtttagttgttaagataatgtaaatccattcatgttcttttaggcaattcactccaaaataatgctcctgttgtag

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|211541853|gb|FL147715.1|FL147715
EST:     CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAG                         GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
genomic: CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
EST: gi|78091048|gb|DV519422.1|DV519422
EST:     CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAG                         GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
genomic: CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
EST: gi|7145217|gb|AW506698.1|AW506698
EST:     CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAG                         GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
genomic: CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
EST: gi|211541851|gb|FL147713.1|FL147713
EST:     CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCVTCTTAGTCAG                         GAGRAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
genomic: CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
EST: gi|211153097|gb|FL147716.1|FL147716
EST:     CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAG                         GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
genomic: CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
EST: gi|78120827|gb|DV539211.1|DV539211
EST:     CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAG                         GAGGAGCTTCCAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA
genomic: CTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCA

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: 142

GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

GATAGACCACATCTTGGGTTTCTTTAGGATATGGGAGCTTCCAGATCATGCTGCAACAGGTTTAGTTGGGAAATTTAGACCTTCCATCCCTCTTAGTCAGgttagtttct ... taacttccagGAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG