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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgttattcttttcatgtttgaactaatccactagtgggttttatatcgtgttttcgtgtatgggtgatgtagaatactttgtgatgctcagatct...

Basic information

species Zea mays
transcript GRMZM2G003734_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003734_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g14654.3 (Oryza sativa), 5'ss of exon 5
GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgttattcttttcatgtttgaactaatccactagtgggttttatatcgtgttttcgtgtatgggtgatgtagaatactttgtgatgctcagatct---------
||| || || ||||| || || ||||||||||| ||||||||||| |||||||||| ||| ||||||||||| || || ||||| ||||| || || ||||| || || || ||| | || || | | ||| ||| | ||| || | | | ||||||| |||| | ||||||
GAAATTAATTGCAAGCCAGATTAAGAACGATGAGCCTAAAGGGCTTCAGAGGGAATTCTTTCTTTACTTTGTGCCACGGCGCACAGTTGCCTGCGAAAAGgtgactattgtt---ttcgtactttgctggttctatt-----gttctatct-gtggcttaggattcaattatattagaataatttgctagcctcagacacaattcaatt

upper sequence: GRMZM2G003734_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G35210.1 (Glycine max), 5'ss of exon 4
GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgttattcttttcatgtttgaactaatccactagtgggttttatatcgtgtt--ttcgtgtatgggtgatg-tagaatacttt-gtgatgctcagatct--
|| ||||| | | || | || |||| | | ||||| || || || ||||| |||| ||||| |||||||||||||||| ||||||||| ||| || || || | ||| || |||| | || | | | || | | | || || ||| | || | || | |
GAGATTCATATGTTCTAATATTCATAATGATGTATCGAAAGGACTGCAAAGAGAATATCATGTTTATTTTGTCCCTCGCCGCACTGTTGTTTGTGAGAAAgtaagc----tttccttggaattgaatctattctggacttgggcatgatgtttttctgttttatatctctatgccaacagcataaatcagtatttttcttgtgtag
















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|76292771|gb|DV032339.1|DV032339
EST:     GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAG                         ATCCTGGAGGAAGAGAAAGTTCATCCGAAACTGACATTCGG
genomic: GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGG
EST: gi|148972311|gb|EE023217.2|EE023217
EST:     GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAG                         ATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
genomic: GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
EST: gi|91049806|gb|EB160224.1|EB160224
EST:     GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAG                         ATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
genomic: GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
EST: gi|148963504|gb|EE014525.2|EE014525
EST:     GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAG                         ATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
genomic: GGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
EST: gi|32932185|gb|CF036997.1|CF036997
EST:     TACCTCGCCGCACTGTTGCTTGTGAGAAG                         ATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
genomic: TACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
EST: gi|33091408|gb|CF051402.1|CF051402
EST:     ACCTCGCCGCACTGTTGCTTGTGAGAAG                         ATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC
genomic: ACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCC

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), 49 (downstream exon)
Score: 123

GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 124

GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 136

GAAGTTCATCGCAAGTCAAATCAAGAACGATGAACCTAAAGGGCTCCAGAGGGAATACTTCCTTTACTTTGTACCTCGCCGCACTGTTGCTTGTGAGAAGgtatctgtta ... gcatctgcagATCCTGGAGGAAGAGAAAGTTCATCAGAAACTGACATTCGGAGAATATCCCTTATATCTAGTTCCATTGGATGATGATGTCTTGTCTCTTGAACTTGACC