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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttagcattcatatttctgaggtgttctgttgtctataatatgtattccttggtgaatgttttactaacatttgtgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA

Basic information

species Zea mays
transcript GRMZM2G025231_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 6
gtaagatttagcattcatatttctgaggtgttctgttgtctataatatgtattccttggtgaatgttttactaacatttgtgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA
|||||||||  |   |||||||||||| |  |||  |    |   ||| || |  |   |    ||||  ||||||||||  |  | ||||||||||||||||| ||||||||||| || || || || |||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||
gtaagatttgcc--ccatatttctgagatactctcctacacaagttatttaattttc--ttgcagtttatctaacatttgcttgttacagATCAACATGAAAGGCTTGGATGGTATCCAAGGCCCCATCTATGTTGGTACTGGATGTGTCTTTAGAAGGCAGGCATTGTATGGTTATGATGCCCCCAAAA

upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 10
----------------gtaagatt-tagcattcatatttctgaggtgttctgttgtct-ataatatgtattccttggtg----aatgttttactaacatttgtgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA
                 | | |||    ||||  |  | |||   | |||| |  ||| |||| ||  |||   | ||     ||   |    |   |  | |  | | ||||| |||||||||||||| ||||| ||||| || || || |||||||| ||||||||||| || |||||||| ||  |||||||||||||||| || || |
gtgagcatgcacttctttcatattgcctcatttcttctgctgttcttttctttgttctcataacatcaattatcttgtatgccaagactaatttgcaaactctactttccagATTAACATGAAAGGTTTAGATGGCATTCAAGGACCCATATATGTTGGGACTGGATGTGTGTTCAGAAGGCAAGCGCTATATGGTTATGATGCTCCAAAGA

upper sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 10
gtaagatttagcattcatatttctgaggtgttctgttgtctataatatgtattccttggtgaatgttttactaacatttgtgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA
|||||  |     |    || |||  | || |   ||   ||   ||    ||   |   || ||  ||  | |  ||| | |     |||||||||||||||| ||||| || ||||| || || |||||||| |||||||| ||||| |||||||| |||||||| |||||| ||||||| || ||||
gtaagcctgcagttctccatatctt-gatgctagttttgatagtttagagcttttctatcgattgacttggtcat-tttatatgcactagATCAACATGAAAGGCTTGGACGGAATTCAAGGACCCATTTATGTGGGTACTGGGTGTGTCTTTAGAAGACAGGCATTCTATGGTAATGATGCTCCAAAAA

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|194717185|gb|FK934338.1|FK934338
EST:     GGATTGATCGCCATGACTGATATGCTAACCGGAATGTTGTCTTTTTTGAT                         ATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGT
genomic: GGATTGATCGCCATGACCGATATGCTAACCGGAATGTTGTCTTTTTTGATgtaagattta ... tgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGT




















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: 47 (upstream exon), 48 (downstream exon)
Score: 147

TTTACTAGGAAAGAAGGTTTGCTATGTACAGTTCCCTCAAAGATTTGATGGGATTGATCGCCATGACCGATATGCTAACCGGAATGTTGTCTTTTTTGATgtaagattta ... tgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

TTTACTAGGAAAGAAGGTTTGCTATGTACAGTTCCCTCAAAGATTTGATGGGATTGATCGCCATGACCGATATGCTAACCGGAATGTTGTCTTTTTTGATgtaagattta ... tgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TTTACTAGGAAAGAAGGTTTGCTATGTACAGTTCCCTCAAAGATTTGATGGGATTGATCGCCATGACCGATATGCTAACCGGAATGTTGTCTTTTTTGATgtaagattta ... tgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1816

TTTACTAGGAAAGAAGGTTTGCTATGTACAGTTCCCTCAAAGATTTGATGGGATTGATCGCCATGACCGATATGCTAACCGGAATGTTGTCTTTTTTGATgtaagattta ... tgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctataatatgtattccttggtgaatgttttactaacatttgtgttgtgcagATCAACATGAAAGGTTTGGATGGTATTCAGGGTCCAATTTATGTTGGTACTGGATGTGTATTTAGAAGGCAGGCATTATATGGTTATGATGCCCCCAAAA
                                 tactaac  putative branch site (score: 1816)
     tataatatgtatt  TA-rich tract