Sequence
atgc intronic sequence ATGC exonic sequencegtgagctcaatcttcatttgcctacgcatcattctactttctgcattataattcagctgaagctcttttgacttttttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G089454_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 5
gtgagctcaat-cttcatttgcctacgc--atcattct---------actttctgcattataattcagctgaagctcttttgacttttttgt-tttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT----------------------------
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gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagTGGTCTT---TCTCATGTATTTCAGAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGT
upper sequence: GRMZM2G089454_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g49980.1 (Oryza sativa), 3'ss of exon 5
gtgagctcaat-cttcatttgcctacgc--atcattct---------actttctgcattataattcagctgaagctcttttgacttttttgt-tttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT--------------------------------------------------
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gtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtctt---tctcatgtatttcagAGGCCTGGAATTGATAAAGGACCGGGAAGTTTGCTGCTACATGATCTCTTGCAAGGACTCTGTAAACATAGATGTTGTCATTGATTGGCTTATCAAGCACMapped 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|76017536|gb|DT944706.1|DT944706EST: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACT TGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
EST:
gi|60338272|gb|DN205245.1|DN205245EST: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACT TGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST:
gi|211033084|gb|FL322683.1|FL322683EST: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCATTGGTTGATCAACT TGGACTGGAATTGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCTG
EST:
gi|58029961|gb|CX725388.1|CX725388EST: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCANGCATTGGTTGATCAACT TTGGACTGGAATTGATAAAGGACCGCGAAGTTTTGTTGCTACATGATCTCC
genomic: AAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagT-GGACTGGAATCGATAAAGGACCGCGAAGTTT-GTTGCTACATGATCTCC
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:
33 (upstream exon),
48 (downstream exon)
Score:
101TGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
Block sizes:
33 (upstream exon),
49 (downstream exon)
Score:
123TGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
Block sizes:
33 (upstream exon),
49 (downstream exon)
Score:
71TGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
Block sizes:
33 (upstream exon),
49 (downstream exon)
Score:
67TGCTGACAAAACAGTCTTTAGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGTGCTTTCGAAGCAGGCATTGGTTGATCAACTgtgagctcaa ... ttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctactttctgcattataattcagctgaagctcttttgacttttttgttttcagTGGACTGGAATCGATAAAGGACCGCGAAGTTTGTTGCTACATGATCTCCT
ttttgac putative branch site (score: 67)
ctcttttgactttttt CT-rich tract
attataattca TA-rich tract