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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgcattagatttagttttcactcaatcagtattgatttccatcagatgaagatcagtgattttttgggtattaatgtttatattattttgtttgatatag

Basic information

species Zea mays
transcript GRMZM2G056393_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056393_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 5'ss of exon 9
GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgcattagatttagttttc-----actcaatcagtattgattt----ccatca--gatgaagatcagtgattttttgggta--------------ttaatgtttatattattttgt--ttgatatag
|||||||||||||||||||||||||| ||||||||||||||||||||||  |||| | ||   |     | | | | ||||||  |||      ||||  |  |  |||   |   ||| |  | |               |||| | |   ||||| |||  |  ||||||
GTTCCTCGCTTGGTAAGGATGCACTCCAATGAGATGGAGgtaagttgcaccagatgttgtaaccaaaataattactaagtattagtttgatctgatcattggagttgattgtttcctttataagcaaatccacccctaggctaatatcttctttattctgtggtcaatatag

upper sequence: GRMZM2G056393_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G16460.1 (Glycine max), 5'ss of exon 9
GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgcattagatttagttttcactcaatcagtattgatttccatcagatgaagatcagtgattttttgggtattaatgtttatattattttgtttgatatag
||||||||||||||  ||||||| ||| |||||||||||||  |||     || || ||| | |   | || |   |||| | ||    ||   ||     |  |||    || | |||   ||||| ||   |  ||  | |  
GTTCCTCGCTTGGTTCGGATGCATTCTGATGAGATGGAGgtttgtttttagagtttcagtatcc---ctattaa-gttgaatgcccctggaaacagtgtttttttttaaaagggagtaagagttataataagatacttttttt--

upper sequence: GRMZM2G056393_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 5'ss of exon 9
GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgcattagattta-gttttcactcaatcagtattgatttccatcagatgaagatcagtgattttttgggtattaatgtttatattattttgtttgatatag
||||||||||||||  ||||||| ||||||||||||||||| ||||   || | || |    |||||   |  || ||  ||    ||   || |  |    |   |  ||| | |     |   | |  | |   || |   |  
GTTCCTCGCTTGGTTCGGATGCATTCTAATGAGATGGAGgttagtt---tttgcttgacacattcacctcactagcat--atgcaaatgcaattattagttttttctccttgag-agggtaggccaaacaaatcctttgggagtc-

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|32930091|gb|CF034903.1|CF034903
EST:     GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
EST: gi|67019503|gb|CO448252.1|CO448252
EST:     GTTCCTCGCTTGGTAAGGATGCACTCNTA-TGAGATGGAG                         GATATTCAAGAAGCATATGCTGGGCCAAAT-GTTGCTGTTTTTGGTGGTGA
genomic: GTTCCTCGCTTGGTAAGGATGCACTC-TAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGG-CCAAATTGTTGCTGTTTTTGGTGTTGA
EST: gi|91874831|gb|EB404788.1|EB404788
EST:     GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
EST: gi|211410070|gb|FL355701.1|FL355701
EST:     TAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: TAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
EST: gi|118406757|gb|EH038205.1|EH038205
EST:     GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
EST: gi|211409847|gb|FL347405.1|FL347405
EST:     TAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: TAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
EST: gi|67017174|gb|CO445923.1|CO445923
EST:     GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
EST: gi|211430479|gb|FL350077.1|FL350077
EST:     TAAGGATGCACTCTAATGAGATGGAG                         GATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT
genomic: TAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGAT

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: 49 (upstream exon), 49 (downstream exon)
Score: 247

GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 220

GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 252

GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 236

GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgca ... tttgatatagGATATTCAAGAAGCATATGCTGGCCAAATTGTTGCTGTTTTTGGTGTTGATTGTGCATCAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTCGCTTGGTAAGGATGCACTCTAATGAGATGGAGgtaagttgcattagatttagttttcactcaatcagtattgatttccatcagatgaagatcagtgattttttgggtattaatgtttatattattttgtttgatatag

- - - - - - -  AGGATG
- - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - GATGGA