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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcatgcattttgagacaaatcctcgcgttttattcccctttcttcttttttttttacttaccagtgccatgcgtgtctacag

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 9
CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcatgcattttgagacaaatcctcgcgttttattcccctttcttcttttttttttacttaccagtgccatgcgtgtctacag
| || |||||||  | |||| ||||||||||| |  | |||||||| || || |||||||||||||| |||||||| || ||||||||  |||  | ||    | |        | | | |    |     ||  |  |  ||  |||| || |   |||  ||       
CCCTCAAGTCCAGAAGGTTGCTGGAAGATATGTCTTCACGGGGTGTAAAGTATGTAGATTGCTACGGGGTTGACAATGCACTGgtgaggacattaacttccccataggataatccatataaccttctgcgttttctcctcattcgcttatcaatattatgtatgcag----
















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|40337292|gb|CK371362.1|CK371362
EST:     CCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG                         GTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGAC
genomic: CCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGAC
EST: gi|32941368|gb|CF046187.1|CF046187
EST:     CCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG                         GTTCGAGTTGCAGATCCTACGTTCTTAGGGTA
genomic: CCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTA
EST: gi|37397991|gb|CF636304.1|CF636304
EST:     CCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTG                         GTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGACATGGGGGCA
genomic: CCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGACAAGGGCGCA

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: 186

CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGACAAGGGCGCATCTTCTGCCGCCAAAGTGGTTAGGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 262

CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGACAAGGGCGCATCTTCTGCCGCCAAAGTGGTTAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGACAAGGGCGCATCTTCTGCCGCCAAAGTGGTTAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 568

CACTGAAGTCCAAGAAGTTGATGGAAGATATGGCCGCGCGGGGTGTGAAATACGTAGATTGCTACGGAGTTGACAACGCGCTGgtgagagcat ... gtgtctacagGTTCGAGTTGCAGATCCTACGTTCTTAGGGTACTTCATTGACAAGGGCGCATCTTCTGCCGCCAAAGTGGTTAGGAAG