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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatttctgcgccaaatagtttcacaagaaatgtaatatatttctttttttttaaaaaaaagatggtggtgataataaacattttgtctttccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT

Basic information

species Zea mays
transcript GRMZM2G477340_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G477340_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g48060.1 (Oryza sativa), 3'ss of exon 6
gtaaaatttctgcgccaaatagtttcacaagaaatgtaatatatttctttttttttaaaaaaaagatggtggtgataataaacattttgtctttccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT
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gtaatatctttacatcgaaaggatttacactggaaattaaatattg---------tagaagaaa-----tggtgctgacaaacatttctgtacactaatgcagAATTGCCGGAGAGATCTTATGGAGCTGACTGCCGTCTGTATGTTCCGGAAAACCCTAAAAACAAGTTCATAAATATTTAT
















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|33099446|gb|CF059406.1|CF059406
EST:     TGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTG                         AATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAA
genomic: TGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAA
EST: gi|33099553|gb|CF059513.1|CF059513
EST:     TGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTG                         AATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAA
genomic: TGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAA
EST: gi|33100318|gb|CF060278.1|CF060278
EST:     TGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTG                         AATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAA
genomic: TGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAA

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: 17 (upstream exon), 46 (downstream exon)
Score: 5

AATCGTGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 15

AATCGTGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 32

AATCGTGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 9

AATCGTGACGATGCTCGCCAGTTCATGAAACACCTTCACCCTGATCTTGGAGTTGgtaaaatttc ... tccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttaaaaaaaagatggtggtgataataaacattttgtctttccaatgcagAATTGCCAGAGAGATCTTATGGAGCTGATTGCCGTTTGTATGTTCCAGAAAACCCTAAAAACAAGTTCATAAATATTTAT
                                  cattttgtctttcc  CT-rich tract
                        tgataataaacatttt  TA-rich tract