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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 32
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 50
gttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgca-atgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC
||| |  || ||| |  |||||| |||| |||| ||| |  |  ||||   |||       |||  | | ||  |||| || ||  |||||||||||||||||||| || ||||||||||| || || || |||||| | ||||| || || ||||| ||| | ||||| ||||||||||| ||||| || |
gtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactga-------ttggctattat--cgtttttggctcatgcagGTGGAGAAGAATGCTGCTGCTGGAAGAACTCCCTCCAGCCTTCCATTATCCACACCTCCGCCAATTGCACCTATACCCTCTCCAAAATTTGCACCTTCAC

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 52
----------------gttggtaatctcagttttgga--ggagtttgagcttgttattttaatt-----ttgtttgaggtacgattga--atttaattac--------gttgtttgcaat----gcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAA---TACCTTCTCCAAAATTGGCACCGTCCC
                  |  |||     ||| |  |  ||| ||||   ||  |||||  |       |||   |  |||  |||||  |||| |  |         | | ||||  ||    |||| ||||||||||||| |||||||||||||| ||||| ||| | ||  || | || || || ||   | |   ||   || |||||||  | || |||||     
gttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCAAGTTTACCGATGCCTACCCCTCCACCGGCATCTTTAAATATATCTTCTCCGGATTTTGCACCTC---

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 53
-------------gttggtaatctcag----ttttggaggagtttgagcttgttattttaatt-----ttgtttgaggtacgattga--atttaattac-----gttgtttgcaat------gcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAA---TACCTTCTCCAAAATTGGCACCGTCCC
               | ||| |  ||     | ||    ||  |||   ||  |||||  |       |||   |  |||  |||||  |||| |  |       ||| ||  ||       |||| ||||||||||||| |||||||||||||| ||||| ||| | ||  || | || || || ||   | |   ||   || |||| ||  | || |||||     
gttgagttaatttacttgtattaccacatgttcttaattgaacttgcattttgtatttctaccggcgattgggagtagtagaattgagtatttgaccattggcaattgattttaacattttggcagATGGAGAAGAATGCTGCAGCTGGAAGAACTCCTTCGAGTTTACCGATGCCAACCCCTCCACCGGCATCTTTAAATATATCTTCCCCTGATTTTGCACCTC---

upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 33
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 22
------gttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaat-gcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAA---TACCTTCTCCAAAATTGGCACCGTCCC
       ||   ||| ||    ||| |  | |    | ||   ||    |  || |   | | |   |    | |  |     | ||||   | |||| ||||||||||||||||||||||||| || || || ||  | ||  |||| || || |||||     |   ||   |  |||| || ||||| |||||     
gtctgcatttagaatatccaaattg-aaaattccaggattacaatgggtacattttaacaagcagtttcttttcttttcctcctttttgttgttgcagATGGAGAAGAATGCAGCAGCTGGAAGGACCCCATCGAGCTTGCCCATGTCGACACCTCCCCCTTCTTCTCTAAGCCTTTCTTCCCCCAAATTTGCACCAC---

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|12045716|gb|BF727855.1|BF727855
EST:     AGAATGCTAGTGAAGCATTTAGAACCTATATCAAGGATGGGCTAGCTCAA                         GTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTGC
genomic: AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
EST: gi|211104807|gb|FL044860.1|FL044860
EST:     TATATCAGGGATGGGCTAGCTCAG                         GTGGAGAARAATGCAGCASCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
genomic: TATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
genomic: AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
genomic: AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC

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), 48 (downstream exon)
Score: 163

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 36

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 61

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 122

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC
                        attgaatttaatta  TA-rich tract