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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggcgcagttctcctgcgctttcgagattttttttttgtcacagaccaatatcattctgatttctgagtatctatgtattaaggtggttttctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC

Basic information

species Zea mays
transcript GRMZM2G167886_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167886_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 5
gggcgcagttctcctgcgctttcgagattttttttttgtcacagaccaata-------tcattctgatttctgagtatctat-gtattaaggtggttttctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
| || || | | |||| | | | |||| | || ||| | | || | || || | | || || ||||||||| ||||| | | ||||||| ||||||| |||||||||||| ||||||| |||| |||||||||||||| || || |||| | | ||
--------caaactgttaattcagaaaaatgttttacaaaaaaaaacaatgttgaattttgtttcacttttttattacttgccataagaaattattgttgcaatgtagGTTAGATATCATCCATTACATCCTGATATCGTTGCTAGCGGAAGTTTGGATAATGAAGTTTGTCTATGGGATGCTAAAACCTCCCGTTGCATTGGATCAC
















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|18385319|gb|BM418518.1|BM418518
EST:     CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG                         GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
EST: gi|18384882|gb|BM418081.1|BM418081
EST:     CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG                         GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGT
EST: gi|76015702|gb|DT942872.1|DT942872
EST:     CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGT-                         -T-AGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
EST: gi|22489334|gb|BU049257.1|BU049257
EST:     CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG                         GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
EST: gi|87298785|gb|DY470788.1|DY470788
EST:     CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG                         GTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT
genomic: CTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGAT

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: 48 (upstream exon), 41 (downstream exon)
Score: 48

TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 24

TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 31

TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 36

TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTGgtacattacg ... tctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatatcattctgatttctgagtatctatgtattaaggtggttttctgttgcagGTTAGATTCCATCCTCAGCGTTCTGATATTCTTGCTAGTGGAAGTTTGGATTGTGAAGTTCGTCTCTGGGATGCTAAAACATCTCGCTGCACAGCAGAAC
         ttctgat  putative branch site (score: 36)
 ttttctgtt  putative PPT
 tatctatgtattaa  TA-rich tract