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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactccattgataggacactttctcttggtcaacgtcaatttattccattgagaaggattttccccttactgtgggttatttgccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os03g02150.2 (Oryza sativa), 3'ss of exon 17
----------------------------------------------------------------------------------------------gtaactc-cattgatag----gacactttctcttggtcaacgtcaatttattccattgagaaggattt--tccccttactgtgggtt-atttgccaaatct-agTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG
                                                                                              | | ||  |||   ||      |     | | |   | | | |  |||  ||||||| | || |||||  |   |||||| ||| || | ||| | ||||| ||||||| |||||||||||||||||||| |||||  |||||||||||||||||||||| |||||  |||| ||||||||||||||||| |||||| ||||  
gtaaattttcatcctgttgcatgtatactcacagtttacggtattaaatcttcttctagccacatatattctcacactttagtgtatgaaatctgcatcttacatgtgtactctcaatttactatataacttatcttgcattcgttccattaacaatgatttgtttttcttactatggatttacttgtcgaatcttagTCTGCTCTGTTGAAGAAGGCTGAAGATGCTGAGGTTGACACAGCAGAGCAAAGTGCTATAAAATTACGAAGTCAGCAACAAACATCGAGTGCTATTGTCA
















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|33097281|gb|CF057241.1|CF057241
EST:     CTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAG                         TCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAA
genomic: CTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAGgtaactccat ... ccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAA
EST: gi|101401386|gb|EB822370.1|EB822370
EST:     CTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAG                         TCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAA
genomic: CTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAGgtaactccat ... ccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAA

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: 115

TGAAATACAACAGAGAGCAGTTGAATATTTTGAACTAAGCAGGAAAGGTCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAGgtaactccat ... ccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 122

TGAAATACAACAGAGAGCAGTTGAATATTTTGAACTAAGCAGGAAAGGTCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAGgtaactccat ... ccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 107

TGAAATACAACAGAGAGCAGTTGAATATTTTGAACTAAGCAGGAAAGGTCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAGgtaactccat ... ccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

TGAAATACAACAGAGAGCAGTTGAATATTTTGAACTAAGCAGGAAAGGTCCTGCTTTGGCAGATGTGTTGGCTGAAATGCCAAAATTCCCTGAACGTGAGgtaactccat ... ccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattccattgagaaggattttccccttactgtgggttatttgccaaatctagTCTGCACTGTTGAAGAAGGCTGAAGACGCTGAAATTGACACAGCAGAGCAAAGTGCCATAAAGCTACGCAGTCAGCAACAAACATCTAGTGCTCTTGTTG
                         cccttac  putative branch site (score: 77)
                                      ttattt  TA-rich tract