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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatctgtcatcaaaatttctaagaagttcccttgtctaacatgatacattgaacttacaatgctgtttccctaatgttacattcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA

Basic information

species Zea mays
transcript GRMZM2G113137_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 10
gtaagatctgtcatcaaaatttctaagaagttcccttgtctaacatgatacattgaacttacaatgctgtttccctaatgttacattcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA
||||||| | ||  ||| |||||| |     | | | || ||   |||  |||  |||||   |||||||||||||| | ||   ||| | ||||||||||||||||||||||||||||| || ||||| || ||||| ||||||||||||||||| ||||| |||||  | ||||| || ||||| |||||| 
gtaagatttatctccaatatttctgattctgttcatcgtgtatgttgagccatcaaacttg--atgctgtttccctattatttatttcttgcagATCAACATGAAAGGTTTGGATGGTATTCAAGGCCCCATCTATGTCGGTACTGGATGTGTCTTTAGAAGACAGGCGCTGTATGGTTATGATGCCCCCAAAT

upper sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 10
------------gtaagatctgtcatcaaaatttctaagaagttcccttgtctaacatgata----cattgaactta-----caatgctgtttccctaatgttacattcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA
             |      | |   |  | ||  |  |  ||||  || | |    | |||    || | | |||      |||  ||  ||  | ||   ||| |||   ||||| |||||||||||||| ||||| || || || || || ||||| || ||||||||||| ||||||||||| ||  ||||||| || |||||||| || |
gtgagcatgcacttctttcatattgcctcatttcttctgctgttcttttctttgttctcataacatcaattatcttgtatgccaagactaatttgcaaactctactttc---cagATTAACATGAAAGGTTTAGATGGCATTCAAGGACCCATATATGTTGGGACTGGATGTGTGTTCAGAAGGCAAGCGCTATATGGTTATGATGCTCCAAAGA

upper sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 10
gtaagat--ctgtcatcaaaatttctaagaagttcccttgtctaacatgatacattgaacttacaatgctgtttccctaatgttacattcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA
|||||    | ||  || | || |    || | |   ||   ||   |    | ||   ||  | ||  ||  |   | || ||| || ||   |||||||||||||||| ||||| || || || || || ||||||||||||||||| |||||||| ||||| |||||||| |||||  | |||||||| ||||
gtaagcctgcagttctccatatctt---gatgctagttttgatagtttagagctttt--ctatcgat--tgacttggtcattttatatgcac-tagATCAACATGAAAGGCTTGGACGGAATTCAAGGACCCATTTATGTGGGTACTGGGTGTGTCTTTAGAAGACAGGCATTCTATGGTAATGATGCTCCAAAAA

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|87156952|gb|DY401741.1|DY401741
EST:     GGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATCCAGGGGCCCA-TTTATGTGGGTAC
genomic: GGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGG-CCCAATTTATGTGGGTAC
EST: gi|50339235|gb|CO534361.1|CO534361
EST:     GGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACT
genomic: GGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACT
EST: gi|32795886|gb|CD948122.1|CD948122
EST:     GGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGAT                         ATCAACATGAAAGGTTTGGATGGTAACCAGGGCCCAATTTATGTGGGTACT
genomic: GGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACT

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), 43 (downstream exon)
Score: 148

TTTGCTTGGAAATAAAGTTTGCTATGTGCAGTTTCCTCAAAGATTTGATGGGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 359

TTTGCTTGGAAATAAAGTTTGCTATGTGCAGTTTCCTCAAAGATTTGATGGGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 298

TTTGCTTGGAAATAAAGTTTGCTATGTGCAGTTTCCTCAAAGATTTGATGGGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

TTTGCTTGGAAATAAAGTTTGCTATGTGCAGTTTCCTCAAAGATTTGATGGGATTGATCGCCATGATCGATATGCTAACAGAAATGTTGTCTTTTTCGATgtaagatctg ... attcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacatgatacattgaacttacaatgctgtttccctaatgttacattcatacagATCAACATGAAAGGTTTGGATGGTATCCAGGGCCCAATTTATGTGGGTACTGGATGTGTCTTCAGAAGGCAGGCATTATATGGCTACGATGCTCCCAAAA
                                    taatgtta  TA-rich tract