Sequence
atgc intronic sequence ATGC exonic sequencegtatgctctgttacctgctagtattaatactactttactgagttctattgacctaacaattcaaactttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G011404_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g09170.1 (Oryza sativa), 3'ss of exon 5
gtatgctctgttacctgctagtattaatactactttactgagttctattgacctaacaattca---------------------aactttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
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gtatgcattcttgcctgctagt-ttattgctagtgta-tgagctattttgatctaagtttttcttcttctttttttttttggttaactttgtacagATGTCCCTGAAGGTTCTTTCATCGTGAGGGAACACACACCAATGTCCAACTTATTTTCATGCCTATGGTTCAATGAGGTTGATCGATTCACACCTCGTGA
upper sequence: GRMZM2G011404_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G31590.1 (Glycine max), 3'ss of exon 7
gtatgctctgtta-----------cctgctagtattaatact---actttactgagt---tctattgacctaacaattcaaactttct-acagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
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gtatgttctgttaatgatttttgtttttcttctgtcaattctcgaaatttgttgattaaatgtactgaaatgacttataatatcttttgacagATGTACCTGAAGGTTCTTTTATTATCAGAGCACACACTCCGATGTCAAATTTGTTTTCCTGTCTGTGGTTCAATGAAGTTGACCGGTTTACCCCTCGTGA
upper sequence: GRMZM2G011404_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0072g01020.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtatgctctgttacctgctagtattaatactactttactgagttctattgacctaacaattcaaactttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
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gtatgattttgttcaagaatctctctattttttatgctaaatttgcagcttgcatc--tattg-tttccacagctttctttatttg----tttgctctattgacagATGTTCCTGAAGGATCTTTTATTGTGAGAGCACACACTCCAATGTCAAACTTGTTCTCCTGCCTTTGGTTCAATGAAGTTGATCGATTTACTCCTCGTGAMapped 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|7119098|gb|AW497478.1|AW497478EST: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCT ATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
genomic: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
EST:
gi|211160450|gb|FL446939.1|FL446939EST: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCT ATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
genomic: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
EST:
gi|32804682|gb|CD956918.1|CD956918EST: GATCCCAGCAGGCTTCTACCAAGCT ATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCAATGTCCAACT
genomic: GATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
EST:
gi|67013916|gb|CO442665.1|CO442665EST: TGGACTGACATG-TTCAACCCATCGGATCC-ANCATGCTTCTACCAAGCT ATGTCCCTGAAGGCTCCTTTNATCGCA-GAGAGCACACACCGATGTCCAAC
genomic: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTT-ATCGCAAGAGAGCACACACCGATGTCCAAC
EST:
gi|32804547|gb|CD956783.1|CD956783EST: GATCCCAGCAGGCTTCTACCAAGCT ATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
genomic: GATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
EST:
gi|40334682|gb|CK368752.1|CK368752EST: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCT ATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
genomic: TGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACT
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:
47 (upstream exon),
47 (downstream exon)
Score:
73AAGTTCAACCACACAATAATTGACCAGCAATTTGAGTTTTATCAAGCGGATGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
Block sizes:
47 (upstream exon),
45 (downstream exon)
Score:
39AAGTTCAACCACACAATAATTGACCAGCAATTTGAGTTTTATCAAGCGGATGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
Block sizes:
47 (upstream exon),
47 (downstream exon)
Score:
32AAGTTCAACCACACAATAATTGACCAGCAATTTGAGTTTTATCAAGCGGATGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
59AAGTTCAACCACACAATAATTGACCAGCAATTTGAGTTTTATCAAGCGGATGGACTGACAAGGTTCAACCCATCGGATCCCAGCAGGCTTCTACCAAGCTgtatgctctg ... ctttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattaatactactttactgagttctattgacctaacaattcaaactttctacagATGTCCCTGAAGGCTCTTTTATCGCAAGAGAGCACACACCGATGTCCAACTTATTTTCCTGCCTGTGGTACAATGAAGTTGATCGATTCACACCTCGTGA
acctaac putative branch site (score: 59)
ctttctac putative PPT
taacaatt TA-rich tract