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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccatgttcagatgctatacattttgtaaaatattgtcatttacgcgcttctgaaatattgtcatttatccttctgaaatattgtcatttatgcgcttattctttgttgccatgttcagatgctatacattttgtagtatccttttggccagtattaatcactcacctattttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG

Basic information

species Zea mays
transcript GRMZM2G005869_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005869_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g21620.1 (Oryza sativa), 3'ss of exon 2
gtaggccatgttcagatgctatacattttgtaaaatattgtcatttacgcgcttctgaaatattgtcatttatccttctgaaatattgtcatttatgcgcttattctttgttgccatgtt--cagatgctatacattttgtagtatccttttggccagtattaatcactcacctattttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG
                                                                              |      || |||| | || |  | |||||||||| || | |  ||       || |||||  |||   ||| |  | | | |||| | |     |   |||||||||||| |||||||||||||||||  ||||||||||||| ||||| ||||| ||||||||||| ||||| |||||||| |||||
-----------------------------------------------------------------------------gtatgcatttatcatctctgtg--tgttctttgttgtcaagctatcatgcatgttatatttttcagt---cttgtcccaaattttaaacccagtatttacttggcagACAAAATACCGACTTTACCTTGTGTTGGACTTCATAAATGGGGGCCATCTTTTCTTCCAGCTCTACCAACAGGGTTTGTTTAG
















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|60338397|gb|DN205370.1|DN205370
EST:     TGACAAAGGTTGACCATCCTTTCGTCGTGCAGCTGAGGTACTCCTTTCAG                         ACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTC
genomic: TGACAAAGGTTGACCATCCTTTCGTCGTGCAGCTGAGGTACTCCTTTCAGgtaggccatg ... attttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTC




















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: 232

GGTTGTGGAGAAGAATCACACTGAGTACATGAAAGCTGAGAGAGATATACTGACAAAGGTTGACCATCCTTTCGTCGTGCAGCTGAGGTACTCCTTTCAGgtaggccatg ... attttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

GGTTGTGGAGAAGAATCACACTGAGTACATGAAAGCTGAGAGAGATATACTGACAAAGGTTGACCATCCTTTCGTCGTGCAGCTGAGGTACTCCTTTCAGgtaggccatg ... attttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

GGTTGTGGAGAAGAATCACACTGAGTACATGAAAGCTGAGAGAGATATACTGACAAAGGTTGACCATCCTTTCGTCGTGCAGCTGAGGTACTCCTTTCAGgtaggccatg ... attttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

GGTTGTGGAGAAGAATCACACTGAGTACATGAAAGCTGAGAGAGATATACTGACAAAGGTTGACCATCCTTTCGTCGTGCAGCTGAGGTACTCCTTTCAGgtaggccatg ... attttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacattttgtagtatccttttggccagtattaatcactcacctattttggcagACAAAGTACCGACTTTACCTTGTCCTGGACTTCATAAACGGGGGTCATCTCTTCTTCCAGCTTTACCACCAGGGTTTATTTAG
                                    cactcac  putative branch site (score: 273)
                                          cctatttt  CT-rich tract
                           agtattaat  TA-rich tract