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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaataagctatggagcgaaccattttcatagttagtttaacttgtatgaatttgtaaaagacaataattaattgttcaagcaaacgtgcaaaactggtctttgagatgttagttctactactgattttttagtttcctttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC

Basic information

species Zea mays
transcript GRMZM2G114758_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114758_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g09920.2 (Oryza sativa), 3'ss of exon 5
gtaaaataagctatggagcgaaccattttcatagttagtttaacttgtatgaatttgtaaaagacaataattaattgttcaagcaaacgtgcaaaactggtctttgagatgttagttctactactgattttttagtttcctttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC
                                          |||| |||      | |||| |  |   ||         |     | |    || || | |||| |||     |  ||||||    || |||       |||||||||||||||||||||||||||| | ||||||||||||| || ||| ||||||||||||||| | ||||| ||||||||||| ||||| || ||||||||||||
----------------------------------------gtacttctatatgcc-gcaaaacattactttttgaaaacatactttgcttaagtaattgttgtttgggatacagatgttactacatgcttgtta-----tcttctttcagCCCTGTTGGAACACAGTGTGTTTCCAAGGAAGATCGTCATATCGTGCAAAGAAAAGGACTTGCTGTTGTTGATTGTTCGTGGGCGCGATTAAGTGATGTC

upper sequence: GRMZM2G114758_T05 (Zea mays), 3'ss of exon 6
lower sequence: AT5G10070.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaaataagctatggagcgaaccattttcatagttagtttaacttgtatgaatttgtaaaagacaataattaattgttcaagcaaacgtgcaaaactggtctttgagatgttagttctactactgattttttagtttcctttcttt--cagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC
                                                             | ||     || | |||  |  | |  ||       |      |  |||| |  || || ||  |  |||| ||| || |    ||  ||| || ||||| | ||| ||| | || | ||||||  ||  | |  |  |||| |||||||| ||||| ||||||||||| ||||||||| ||| |||||||
-----------------------------------------------------------gtatacctctttttactgt--atcctagggtcatttgttatgacattggatgatgtttttagtatcgtattttgagtctcatgatattggcagTCCAGTTGGTAGACAATGTGTTTCAAGGGAAGACTATGATCTGATTAAAAGGAAAGGATTAGCTGTTGTTGATTGTTCTTGGGCACGTCTAACTGATGTC
















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|88758037|gb|DY542178.1|DY542178
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|26456351|gb|CA827934.1|CA827934
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTGTATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|211261561|gb|FL168251.1|FL168251
EST:     GAGTTGAGAGTGACCAAWVGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCWAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
EST: gi|60347651|gb|DN214624.1|DN214624
EST:     GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAG                         CCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG
genomic: GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAG

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: 41 (upstream exon), 47 (downstream exon)
Score: 126

GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 114

GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 117

GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 55

GAGTTGAGAGTGACCAATGGTTTTGGTGGTGTTGTTCTCAGgtaaaataag ... tttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggtctttgagatgttagttctactactgattttttagtttcctttctttcagCCCTGTTGGAACACAGTGTATATCCAAGGAAGATCATCCTATTGTGCAAAGAAAAGGATTGGCTGTGGTTGATTGTTCCTGGGCACGTTTAAGTGATGTC
                          tactgat  putative branch site (score: 55)
                                ttttttagtttccttt  CT-rich tract
                             tgattttttagttt  TA-rich tract