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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattttgcatacaagctcatcacctgtagaatttcttatatgtttgttcatcttaactggaaatatacttgctgctgatcatgctaccttttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT

Basic information

species Zea mays
transcript GRMZM2G150024_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150024_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36280.1 (Glycine max), 3'ss of exon 1
--gattttgcatacaagctcatcacctgtagaatttcttatatgtttgttcatcttaactggaaatatacttgctgctgatcatgctaccttttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT
   |  || |         | |    ||  |    | | | |||   ||  ||  | |     ||  ||| || |  | ||  |  |   |||||   ||||| |||||| |  | || ||| ||   | |||    ||| | |||||||| ||||| ||||||||| | || ||||| ||||| |||||||||||||| ||
gcaacattactgctggaaacgttcattggtgtggatttgacatgcaagtatattctgaactttaaagtacctgattgt-atgttcttgtgttttgaa-acagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTCAATCCCTGTACATGGTTTCATGT

upper sequence: GRMZM2G150024_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G31320.1 (Glycine max), 3'ss of exon 1
--gattttgc-atacaagctcatcacctgtagaatttcttatatgtttgttcatcttaactggaaatatacttgctgctgatcatgctaccttttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT
   | ||| |      |  |  |||   ||   | || | |||||   ||  || || |     ||  ||| || |  | ||  |  |   |||||   ||||| |||||| |  | || ||| ||   | |||    ||| | |||||||| ||||| ||||||||| | || |||||||||||||||||||||||||| ||
gcaactttactgctggaaatgttcattggtgtgaatt-tgatatgcaagtatattttgaactttaaagtacctgattgt-atgttcttgtgttttgaa-acagGAGATGCTTTGCATAGTCTGAGGACAAACTTACAGGATCCCAACAATGTTTTGCAAAGTTGGGATCCTACACTTGTTAATCCATGTACATGGTTTCATGT

upper sequence: GRMZM2G150024_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G34210.1 (Arabidopsis thaliana), 3'ss of exon 1
-gattttgcatacaagctcatcacctgtagaatttcttatatgtttgttcatcttaactggaaatatacttgctgctgatcatgctaccttttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT
   | ||  || ||| ||  |    |||   || | | || |||||| | |   |  |         |   |||   | |  || |    | | |  ||||| ||||| ||  ||||  || |    |   |  | ||| | || ||||||||||| || |||||| | || ||||||||||| ||||| |||||||||||
aagtattcaatgcaaactgtttggttgtttcatgtttgatttgtttggtaagtatttcctctttgcgaaaggcttaggcttttgtt-tggtatattaacagGTGATGCACTGCACAGTTTGAGAGCTAATCTAGTTGATCCAAATAATGTCTTGCAAAGCTGGGATCCTACGCTTGTTAATCCGTGTACTTGGTTTCACGT

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|148934569|gb|EC878617.2|EC878617
EST:     TGCGGTCGCGGTGCTGCTCTGGCCGGGCCGGGTCGTCGCCAACACCGAGG                         GCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCT
genomic: TGCGGTCGCGGTGCTGCTCTGGCCGGGCCGGGTCGTCGCCAACACCGAGGgtgagtcctc ... ttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCT




















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: 46 (upstream exon), 49 (downstream exon)
Score: 146

GGCGCTCGAGTTGGAATGGCGGCGGCAGGGAGGTGGTGGGCGGTGGTCCTTGCGGTCGCGGTGCTGCTCTGGCCGGGCCGGGTCGTCGCCAACACCGAGGgtgagtcctc ... ttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GGCGCTCGAGTTGGAATGGCGGCGGCAGGGAGGTGGTGGGCGGTGGTCCTTGCGGTCGCGGTGCTGCTCTGGCCGGGCCGGGTCGTCGCCAACACCGAGGgtgagtcctc ... ttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

GGCGCTCGAGTTGGAATGGCGGCGGCAGGGAGGTGGTGGGCGGTGGTCCTTGCGGTCGCGGTGCTGCTCTGGCCGGGCCGGGTCGTCGCCAACACCGAGGgtgagtcctc ... ttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 121

GGCGCTCGAGTTGGAATGGCGGCGGCAGGGAGGTGGTGGGCGGTGGTCCTTGCGGTCGCGGTGCTGCTCTGGCCGGGCCGGGTCGTCGCCAACACCGAGGgtgagtcctc ... ttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatcttaactggaaatatacttgctgctgatcatgctaccttttgtccacagGCGATGCTCTATACAGCCTGCGGCAGAGCTTGATAGATACGAACAATGTCTTGCAGAGTTGGGATTCCACTCTTGTTAATCCATGTACATGGTTTCACGT
                                         ccttttgtcc  CT-rich tract
               aaatatactt  TA-rich tract