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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattttctaatatattaaattgctcaagccgtggaaatatttaaatttggaaaaaaatcttgacttcttcattttatatag

Basic information

species Zea mays
transcript GRMZM2G172410_T01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G172410_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os03g06720.1 (Oryza sativa), 5'ss of exon 20
GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattttctaatatattaaattgctcaagccgtggaaatatttaaatttggaaaaaaatcttg-acttcttcattttatatag
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GTTGAGCATCTTGTATCAGAAATTGTAGACACGGGACTGGGAAAGCAAgtgagaattcgcttgttggcta--ttactaaattcatcaaattactttaatttggaagcaaatcttttagcctttcattttttgcag
















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|78026627|gb|DV495014.1|DV495014
EST:     GGTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAA                         ATATCTAAAATAAGACCATCCCTTTCATTT-TTGGAGCAGAGGAAATAATG
genomic: GGTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATG
EST: gi|60359779|gb|DN226752.1|DN226752
EST:     GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAA                         ATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATG
genomic: GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATG
EST: gi|32864480|gb|CF004162.1|CF004162
EST:     GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAA                         ATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATG
genomic: GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATG

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), 48 (downstream exon)
Score: 32

GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATGAGTCGTGTGACAGCACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 82

GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATGAGTCGTGTGACAGCACAAG


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

GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATGAGTCGTGTGACAGCACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 20

GTTGAGAATCTTGTATCAGAAATCGTTGACATGGGACTAGGAAAACAAgtaagaattt ... ttttatatagATATCTAAAATAAGACCATCCCTTTCATTTATTGGAGCAGAGGAAATAATGAGTCGTGTGACAGCACAAG