Sequence
atgc intronic sequence ATGC exonic sequencegtgacgcctgcgcgacacacacacatagccatcagctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g39100.1 (Oryza sativa), 3'ss of exon 4
-----------------gtgac-gcctgcgc-gacacacacacatagcc---atcagctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
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gtagccatctgcgtactgtagccacccgagctgaatcagttcgatgatctacatgatcttgacatgtaatgtattcaagctgaaccgattcagctgatgaaactgtatt-tgtttcagGTGTTCTGCTGCTTTGGTAACTCGGTGGCTTCAACCAGGTTCCTGCTGCAAGATGAGTTCAACATTCAGACAACCCAGTGCGACAACTGCATCATT
upper sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G63830.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgacgcctgcgcgacacacacacatagccatcagctttgtctg--tcaatcggataatccgcaattcggttgc-tgaccacgctcccttct--ctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
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gtgatgttcttgatattttggcatttaaa-acctgcttgcaataattcaatagatctcttcatgattcttatgaattagcatttgcaattgaaattttcagGTCTTCCTTTGCTTCGGAAACTCTGTGGCCTCTACCCGCTTTCTTCTGCAGGATGAATTCAACATCCAGACAACACAATGCGACAATTGCATAATT
upper sequence: GRMZM2G065696_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0025g00130.t01 (Vitis vinifera), 3'ss of exon 4
--gtgacgcctgcgcg-acacacacacatagccatc---agctttgtctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
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gtgtaacaaattcatggattcttttagtcagttcactgaggctttgtcaattatcctgatg--tgacaattattccaagcttcttttccactttttgtttagGTTCTCCTCTGCTTTGGAAATTCGGTAGCATCAACCCGCTTTCTGTTGCAAGATGAGTTCAACATACAGACAACAAAATGTGACAATTGCATCATTMapped 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|14242658|gb|BG840354.2|BG840354EST: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST:
gi|51592820|gb|CV071966.1|CV071966EST: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST:
gi|51592771|gb|CV071917.1|CV071917EST: GCGGCAAGTGCGGCGAGAACCAGTGCCCGGAAGTATGCCTTGCAACCGAG GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST:
gi|16918930|gb|BM073956.1|BM073956EST: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST:
gi|47961905|gb|CN844614.1|CN844614EST: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
EST:
gi|32919836|gb|CF024648.1|CF024648EST: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG GTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCCACCCGGTTCCTGCTGCAG
genomic: GCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAG
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:
48 (upstream exon),
39 (downstream exon)
Score:
9GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
211GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
262GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
6GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAGgtgacgcctg ... tctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtcaatcggataatccgcaattcggttgctgaccacgctcccttctctctcagGTGTTCTGCTGCTTCGGCAACTCGGTAGCTTCAACCCGGTTCCTGCTGCAGGACGAGTTCAACATCCAGACAACGCAGTGCGACAACTGCATCATC
tgctgac putative branch site (score: 6)
ccacgctcccttctct CT-rich tract
ataat TA-rich tract