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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccatacagggctggcataacattcattttgtacatatattgggtaaatctctattatacctatgcatatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG

Basic information

species Zea mays
transcript GRMZM2G315806_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315806_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g05806.1 (Oryza sativa), 3'ss of exon 4
---------------------------gtatgttcca-tac-----agggctggcataacattcattttgtacatatattgggtaaatctctattatacctatgcatatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG
                           |||  | | | ||      |   ||  ||   | |    ||| ||  ||        || | || ||| |  | ||  | |||| ||||||||||||||||||||  | |||||||| |||||||||||||||||||||||||||||||| ||   |||| |||||||| | |||||||| |
gtatgttcttttttttttatagtgatggtacttcctaatatttgtgaaatctttcacctcttatgctttatagctaggacttacaattttccatttt--caattaacatttgcagAACAAGATTCAACCAGGAGTACCAAAACCGCGCTTGTTTACTGTGGGTCGTCTTGATGTTGCTACAAGTGGTTTGATAATAATTACAAATGACG

upper sequence: GRMZM2G315806_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G39140.1 (Arabidopsis thaliana), 3'ss of exon 3
---gtatgttccatacagggctg-gcataacattcattttgtacatatattgggt---aaatctctattatacctatgcatatttacagAACAAGATTCAA-----CCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG
     |  ||   |       |    | ||| ||   |||  |  ||| || | |   ||| ||   ||  |        | ||| ||    | |||  ||     || |||   || ||||| ||| | |||||||| ||||||||||||||||||||  | ||  ||||| | || ||||||||||
gtaagacattttgttttcctgtacataaaacgttgtcttttaaagtatgttagattagaaaacttggtttaagaatcttgtctttgcaatgtagGATAAAAGGAATCCGGGGACTCCCAAACCTCGCCTTTTTACTGTTGGTCGTCTTGATGTTGCCACAACGGGATTGATAGTTGTTACAAATGATG
















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|78111429|gb|DV529826.1|DV529826
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGT
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGT
EST: gi|71310508|gb|DR791549.1|DR791549
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTT
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTT
EST: gi|149079210|gb|EE168172.2|EE168172
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTNCA-CCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCG
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATT-CAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCG
EST: gi|149083253|gb|EE172532.2|EE172532
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTCAACCAGGGTTGCCCAAACCACGCTTGTTTACTGTGGGTCGT
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGT
EST: gi|71446099|gb|DR827149.1|DR827149
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGT
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGT
EST: gi|148938500|gb|EC882821.2|EC882821
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTCCAACCAGGGTTGCC
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTC-AACCAGGGTTGCC
EST: gi|101386864|gb|EB815449.1|EB815449
EST:     AGAGTCAAAATCTGTTGTCTCCTTTATTTA-TGATTATTTGAAGGGCTGG                         AAACA-GATTCAACCAGGGTTGCCAAAAC
genomic: AGAGTCAAAATCTGTTGTCTCCTT-ATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAA-CAAGATTCAACCAGGGTTGCCAAAAC
EST: gi|71306649|gb|DR789484.1|DR789484
EST:     AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGG                         AACAAGATTCAACCCAGG-TTGCCAAAACCACGCTTGTTTACT
genomic: AAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACC-AGGGTTGCCAAAACCACGCTTGTTTACT

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: 45 (upstream exon), 47 (downstream exon)
Score: 58

GTACATTTGCTCATGTGGTGAAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 161

GTACATTTGCTCATGTGGTGAAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

GTACATTTGCTCATGTGGTGAAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 65

GTACATTTGCTCATGTGGTGAAGAGTCAAAATCTGTTGTCTCCTTATTTAATGATTATTTGAAGGGCTGGgtatgttcca ... atatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattttgtacatatattgggtaaatctctattatacctatgcatatttacagAACAAGATTCAACCAGGGTTGCCAAAACCACGCTTGTTTACTGTGGGTCGTCTTGATGTTGCCACGGCTGGTCTGATAATAGTCACAAATGATG
     ttttgtacatatatt  TA-rich tract