Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 3
gtttgtgcttgccacttggttcatctttcttcttgacacacctcgttt----------tttatcctaccaaatgtgcgtgtat-atatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
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gtacgcaccatttccctggtgcatcct-ctttttgatgcatctttcttgagtgacatattgatcgcactaattgcatcggtctgattctactttctagGCTCGCTACTTCTTCCAGCAGCTTATCTCGGGAGTCAGCTACTGCCATTCAATG
upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 3
gtttgtgcttgccacttg-gttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
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gttcttatctattcctttcatgcatttttgttgcagtgctgttgcagttaccg-cttaccatttatgtctat-tatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATG
upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 3
gtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
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-------gttcttatctgttgcattcattcatttgtgtaatgctgctgcatatgcctttta-tgtctgtttttttttatgctgc-agGCGCGCTTCTTCTTCCAACAACTTATATCAGGAGTTAGCTACTGTCATGCAATG
upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 3
-gtttgtgcttgccacttggttcatctttcttcttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
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gttcttttctattcctttcatgcatttttgttgcagttctgttgcagttactg-cttaccattaatgcctat-tatgttttgttgcagGCACGCTTCTTCTTCCAACAACTTATATCAGGGGTTAGCTACTGTCATGCAATGMapped 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|211022079|gb|FL377464.1|FL377464EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCTTCCAACAACTCAT
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCAT
EST:
gi|211499753|gb|FL295241.1|FL295241EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST:
gi|211499759|gb|FL295247.1|FL295247EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST:
gi|6022633|gb|AW067445.1|AW067445EST: GNGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST:
gi|148932906|gb|EE285698.2|EE285698EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST:
gi|211204702|gb|FL178018.1|FL178018EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTT
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTT
EST:
gi|78107855|gb|DV526273.1|DV526273EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCA
EST:
gi|211108565|gb|FL429107.1|FL429107EST: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAG GCTCGCTACTTCT
genomic: GTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCT
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),
49 (downstream exon)
Score:
101TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
76TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
94TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
84TATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATGAGgtttgtgctt ... atctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgacacacctcgttttttatcctaccaaatgtgcgtgtatatatatctttccagGCTCGCTACTTCTTCCAACAACTCATTTCAGGAGTAAGCTACTGCCATTCAATG
tcttgac putative branch site (score: 84)
tatctttcc putative PPT
tgtatatatatcttt TA-rich tract