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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctcctagttcagacatttcttcactgtgcttcatgagatcttagcatccttttttcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA

Basic information

species Zea mays
transcript GRMZM5G836588_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 3'ss of exon 12
-------------------gtacc--tcctagttcagacatttcttcactgtgcttcatgagatct--tagcatccttttttcctcta-----tagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA
                    |||   |   |  |   |  |||| ||| | |   |  |||||| |   |  ||| ||| ||  |  |     ||||| |||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| ||||| || |||||||| ||||| |||||
gtattacctagctcaacccatactgatatcatcttttatgtttcatcagtatctgtattgagatgtagcattatcttttattaattaaaaaactagGTTTGGAAGAAAGTTGTCTACGTGGATAGGCTTGTGCATCTGTTCAGATATGTACCACGCGAACAACTAACTATTCCTGATTTTGTCTTTCA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 13
-------------gtacctcctagttcagacatttcttcactgtgcttcatgagatcttagcatccttttttcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA
              |   | |   || |   |  || |   |||| ||  |    |  |   ||      ||    |  |||| ||||||||||| |||||||| ||| | ||| ||||||| |||||||| ||||| || || ||  | || || || || ||||| |||||
gtacagtagtagaatttatgcatatttaatgacctcatatgtgtgttt-gtatatttgtgttattaaaagttgactttcagGTTTGGAAGAAAGTGGTATATGTTGATCGCCTTCTGCAGCTCTTCAGATACGTACCTCGTGAACAGTTGACCATCCCAGATTTTGTGTTTCA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G06730.1 (Glycine max), 3'ss of exon 14
-------------------gtacctcctagttcagacatttcttcac-tgtgcttcatgagatcttagcatccttttttcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA
                    ||    |   ||  ||| | | |       |  |  ||  | | ||| ||       ||    | ||||| ||||||||||| |||||||| ||||| ||  | ||||| |||||||||||||| || || ||| | || || || || ||||| |||||
gtgcgttatgaattggattttattaacagatttggacctatttaaggacatcttatatatgttattatcaatgacgattaacttttagGTTTGGAAGAAAGTGGTATATGTTGATAGACTACTCCAGCTCTTCAGATATGTACCCCGTGAACAATTGACCATCCCAGATTTTGTCTTTCA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 3'ss of exon 13
------------------------------------------gtacctcctagt--tcagacatttcttcactgtgct-tcatgagatcttagcatccttttttcctctata-gGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA
                                           ||    | |||  |   | |    |  | | |||| ||||    |  |  |||           | ||| ||| |||||||||||||||||||  ||  | ||| |||||||||||| ||| || || || ||||| || ||||| || ||||||||||| ||
gtaaagtcctgaattatttcaaagtcccaaccttttccgccgatagactcgagtcattctaaagaagtctaatttgctgtcattttcttgttccatttcgaaaaatccgataagGTATGGAAGAAAGTTGTATATGCAGACCGACTTCTGCAGCTGTTCAAATACGTTCCTCGTGAGCAGCTGACAATCCCAGACTTTGTTTTCCA

upper sequence: GRMZM5G836588_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 12
------------gta-cctcctagttcagacatttcttcactgtgcttcatgagatct--tagcatccttttt---------------------tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA
            ||| |||||| |  || |   || |   |||  ||   |||  |||  | | |  ||| ||                     |  ||| ||||| ||||||||||| |||||||| ||  | ||  |||||||||||||||| || ||||| |||||  | ||||| || |||||||| |||||
gtaagtccaaaagtatcctccttgaccaaatgattatatcctgacctctgtgacttctgtttgaaagcttattgtaagtgaaattgttgggaaatggtctctagGTGTGGAAGAAAGTGGTATATGTTGACCGACTCATGCAGCTGTTCAGATACGTTCCACGTGAGCAGTTGACAATCCCCGACTTTGTGTTTCA

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|211406752|gb|FL443984.1|FL443984
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
EST: gi|211075806|gb|FL464165.1|FL464165
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
EST: gi|148929297|gb|EC875052.2|EC875052
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
EST: gi|78125404|gb|DV543788.1|DV543788
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
EST: gi|94478486|gb|EB707444.1|EB707444
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
EST: gi|211124589|gb|FL474104.1|FL474104
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
EST: gi|76286117|gb|DV025685.1|DV025685
EST:     TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAG                         GTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT
genomic: TGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATAT

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: 43 (upstream exon), 49 (downstream exon)
Score: 51

GCAATTTATGTACTCCACCCAACGTTGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

GCAATTTATGTACTCCACCCAACGTTGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

GCAATTTATGTACTCCACCCAACGTTGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GCAATTTATGTACTCCACCCAACGTTGGGTTTGAGAACAGCTGTTTTGGCAATGCAAATGTTTGTAGATGGAGAGgtacctccta ... tcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagacatttcttcactgtgcttcatgagatcttagcatccttttttcctctatagGTCTGGAAGAAAGTTGTATATGTGGATAGGCTTGTGCAGCTGTTCAGATATGTACCACGCGAGCAACTTACAATTCCTGACTTTGTTTTTCA
                             tcttagcatccttttt  CT-rich tract
                                        tttttt  TA-rich tract