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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatttgtcaaatagtttttatctatgtattttactattccatatcactgtagtttctttgaaactatttatattttcttagtgctattttcccacttgcctcccccctttgttgttgttgttgttgatatgtggtacccaaattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG

Basic information

species Zea mays
transcript GRMZM2G164265_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 8
gtatgcatttgtcaaatagtttttatctatgtattttactattccatatcactgtagtttctttgaaactatttatattttcttagtgctattttcccacttgcctcccccctttgttgttgttgttgt-tgatatg-tggtacccaaattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG
||| ||  ||   |  | ||||   |  |   |  ||   ||  |||| ||||     |    |   |   ||||||   |  || | | | ||         |||      |||   ||  || |||| |||||||    |  ||||||||||||||||| || ||||  |||      || || |||||||||||||| ||| ||||||||||||||||
gtaagctattaatagtttgtttcatttcac-cacattttcatggcata-cactaggactaaaatcttatgctttatacacttgtatttccaattgttgttgcccctattagttttcaagtattttttgtatgatatggcattgtccaaattgtacagCATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG
















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|67020152|gb|CO448901.1|CO448901
EST:     GCCTGGATCGCCTGACGATAAGAAACTTTATCTTATCGATCTCGGTTTAG                         CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
EST: gi|9952315|gb|BE638898.1|BE638898
EST:     GCCTGGATCGCCTGACGATAAGAAACTTTATCTTATCGATCTCGGTTTAG                         CATCCAAGTGGAAAGAGAATAATGGTCATCAT
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCAT
EST: gi|18654924|gb|BM499729.1|BM499729
EST:     GCCTGGATCGCCTGACGATAAGAAACTTTATCTTATCGATCTCGGTTTAG                         CATCCA-GTGGAAAGAGAATAATGGTCATCAT
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCAT
EST: gi|18661950|gb|BM501665.1|BM501665
EST:     GCCTGGATCGCC-GACGATAAGAAACTTTATCTTATCGATCTCGGTTTAG                         CATCCNAGTGGAAAGAGAATAATGGTCATCATGTT
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTT
EST: gi|7145135|gb|AW506616.1|AW506616
EST:     GCCTGGATCGCCTGACGATAAGAAACTTTATCTTATCGATCTCGGTTTAG                         CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
EST: gi|71430775|gb|DR811825.1|DR811825
EST:     GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAG                         CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
EST: gi|67043197|gb|CO469452.1|CO469452
EST:     GCCTGGATCGCCTGACGATAAGAAACTTTATCTTACCGATCTCGGTTTAG                         CATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC
genomic: GCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGC

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: 199

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GTTTGTGCATGGTGATGTGAAACCAGAGAATTTTCTGCTTGGTCAGCCTGGATCGCCTGACGATAAGAAACTTTACCTTATAGATCTCGGTTTAGgtatgcattt ... aattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcctcccccctttgttgttgttgttgttgatatgtggtacccaaattgtacagCATCCAAGTGGAAAGAGAATAATGGTCATCATGTTGATTATGATCAACGGCCTGATATCTTTAG
                          tgttgat  putative branch site (score: 115)
                                            aaattgta  TA-rich tract