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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctccgttccttcgtcttcgtttgttcgttcgttcatgcaatgcatgcggtgaaaatgtgtgtgatatccatgaacgtacgtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG

Basic information

species Zea mays
transcript GRMZM2G062396_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062396_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g56700.1 (Oryza sativa), 3'ss of exon 2
gtgagtctccgttccttcgtcttcgtttgttcgttcgttcatgcaatgcatgcggtgaaaatgtgtgtgat-atccat------gaacgtacgtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG
                        ||  || | | ||  ||  |  |      |||||   ||| |  ||| || |||      |    |  | || |||||   |||||||| || ||||||||||||||||| |||||||||||||||||||| || ||| |||| ||||| ||||| |||||||||||||||||||| |
------------------------gtgagtac-tacggccacactgtatccttggtgattttgttttagatcatgcatctcttaggcaatgtgaacttgcagTATCTGAGCAATGGGAGGTTCAAGAACGCGGATCACCAGGCGGTGGTGAACTCCGACTGCTGCCGGCTGTCGATCGCGACGTTCCAGAACCCGGCGCCGG

upper sequence: GRMZM2G062396_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G05450.2 (Glycine max), 3'ss of exon 2
gtgagtctccgttccttcgtcttcgtttgttcgttcgttcatgcaatgcat-gcggtgaaaatgtgtgtgatatcc----atgaacgtacgtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG
 |   | |  |   |  |   |   || ||| |  |||  |     |   |     |  |||| |||    | |       ||   | || |   |||||   |||||||| || ||||||||||| || || ||||| ||||||||||||||  |    |||||  ||||||| ||||| || || ||||| || ||  
ttatttttatgaagcagcaagtctattggtttgaccgtgtactttgtttttcataatttaaatttgttcatttttttgtggtgggtgcacatgaatgcagTATCTGAGCAATGGAAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCAAACCATAGCCGTTTGTCCATAGCCACTTTTCAAAACCCAGCACCAA

upper sequence: GRMZM2G062396_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g14310.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtctccgttcctt-cgtcttcgtttgttcgttcgttcatgcaatgcatgcggtgaaaatgtgtgtgatatccatgaacgtacg-tacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG
||||||     |||  | | | ||| | | || | |    |||  || |       | | |   |   | |  ||      ||   |    | ||||   |||||||| || |||||||| || ||||||||||| || ||||||||||| || ||||| ||  |||| || ||||||||||||||||| || || |
gtgagtagtgattctctgcttattcctcttttggattccccatcgaaggggcagaataatataattaattaactctgcattcgattgacgtgggcagTATCTGAGCAATGGGAGGTTCAAAAATGCGGACCACCAAGCTGTGGTGAACTCCGACTGCAGTCGGTTGTCGATTGCCACGTTCCAGAACCCAGCCCCAG

upper sequence: GRMZM2G062396_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0023g03370.t01 (Vitis vinifera), 3'ss of exon 2
------gtgagtctccgt--tccttcgtcttcgtttgttcgttcg-ttcatgcaatgcatgcggtgaaaatgtgtgtgatatccatgaacgtacgtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG
      || |   |||    |  | | || |  | || |  |    ||||||| |  |   |   ||||  | | |||||          ||| |   ||||||   |||||||| || ||||||||||| || || ||||| ||||||||||||||  |    ||| | |||||||| || || ||||| ||||| || || |
tatgtggtcaacatccacaatagtccttcctgatatggtattcaaattcatgctacccgaacc-cgaaagagagagtgattattggtttggtatg---gtgcagTATCTGAGCAATGGGAGGTTCAAGAATGCTGATCACCAAGCGGTGGTGAACTCCAATCATAGCAGACTGTCCATAGCAACATTCCAAAACCCCGCACCGG

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|148993878|gb|EE033912.2|EE033912
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
EST: gi|74233228|gb|DT641142.1|DT641142
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
EST: gi|78115223|gb|DV533611.1|DV533611
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
EST: gi|91054734|gb|EB165152.1|EB165152
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
EST: gi|71766104|gb|DR964041.1|DR964041
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
EST: gi|148953973|gb|EC899362.2|EC899362
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
EST: gi|6012227|gb|AW061769.1|AW061769
EST:     TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCATGGCCAC                         CTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC
genomic: TGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAAC

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: 42 (upstream exon), 8 (downstream exon)
Score: 1

CGTCGGCGGCCTCCAGGCCACGCGCGACGGCGGCCGGACCTGGATCACCGTGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 137

CGTCGGCGGCCTCCAGGCCACGCGCGACGGCGGCCGGACCTGGATCACCGTGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG


Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 50

CGTCGGCGGCCTCCAGGCCACGCGCGACGGCGGCCGGACCTGGATCACCGTGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 304

CGTCGGCGGCCTCCAGGCCACGCGCGACGGCGGCCGGACCTGGATCACCGTGCAGCCCGTGGAGGGCGCCTTCGTCGTCAACCTCGGCGACCACGGCCACgtgagtctcc ... gtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcaatgcatgcggtgaaaatgtgtgtgatatccatgaacgtacgtacgtgcagCTCCTGAGCAACGGCAGGTTCAAGAACGCGGACCACCAGGCGGTGGTGAACTCGGAGTGCAGCCGCCTGTCCATCGCCACGTTCCAGAACCCGGCGCCCG
               tgaaaat  TA-rich tract