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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGTGCTGGTTTCAAGAGCTGCTTTTGTTTTCCCACTATCCTTTGTATCAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtctttaacttagcaacatcttaacttcttatgttctcttgaaacagttgttatgttccttacatgatattggtcattcag

Basic information

species Zea mays
transcript GRMZM2G037342_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037342_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 5'ss of exon 10
CTTGGTGCTGGTTTCAAGAGCTGCTTTTGTTTTCCCACTATCCTTTGTATCAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtctttaacttagcaacatcttaa-cttcttatgttctcttgaaacag--ttgttatgttccttacatgatattggtcattcag
||||||||||||  |||||||||||||||||||||||||||| ||| |  ||||||||||||||||||||  | | |||||||| ||| ||| |||||| || ||| ||| | |||||| |||||||  |||  ||| |||||||  ||  |   | | | ||| ||||  |||| | ||| ||||||
CTTGGTGCTGGTCGCAAGAGCTGCTTTTGTTTTCCCACTATCTTTTTTGGCAAATTTGACCAAAAAAACTGAAGAGGGAAAGATCTCTATTAAGCAGCAAgtgagtgttttatttagcagcatcttaggcttgctatcttctcttataaggggactttcaggttactta--tgatgtgggttattcag
















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|19058280|gb|BM736947.1|BM736947
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|110481107|gb|EE010953.1|EE010953
EST:     AAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTG-TTGGTGGGCGGGTTTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: AAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|71301742|gb|DR786939.1|DR786939
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|76931825|gb|DV172864.1|DV172864
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|76921050|gb|DV168432.1|DV168432
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|87152007|gb|DY396796.1|DY396796
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|20300776|gb|BQ163719.1|BQ163719
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|18964390|gb|BM660978.1|BM660978
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
EST: gi|78119305|gb|DV537689.1|DV537689
EST:     CAAATTTGACCNNNNNNNCTCCAAATGGAAAGATATCTTTTAGGCAGCAG                         GTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG
genomic: CAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTG

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: 46 (upstream exon), 49 (downstream exon)
Score: 95

CTTGGTGCTGGTTTCAAGAGCTGCTTTTGTTTTCCCACTATCCTTTGTATCAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 62

CTTGGTGCTGGTTTCAAGAGCTGCTTTTGTTTTCCCACTATCCTTTGTATCAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

CTTGGTGCTGGTTTCAAGAGCTGCTTTTGTTTTCCCACTATCCTTTGTATCAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 129

CTTGGTGCTGGTTTCAAGAGCTGCTTTTGTTTTCCCACTATCCTTTGTATCAAATTTGACCAAAAAAACTCCAAATGGAAAGATATCTTTTAGGCAGCAGgtaagtcttt ... ggtcattcagGTTATTGTTTGGTGGGCGGGTCTCATGAGAGGTGCTGTGTCTATTGCGTTGGCTTACAATAAG