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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtaggattttcatacttagacccgtttatgctattttccttattccagttagtttagttaatttgcttgtcaagaatcttccttgtactgttcgtt...

Basic information

species Zea mays
transcript GRMZM2G040017_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g55940.2 (Oryza sativa), 5'ss of exon 10
GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtaggattttcatacttagacccgtttatgctattttccttattccagttagtttagttaatttgcttgtcaagaatcttccttgtactgttcgtt-
|||||   ||||||||||||||||||||||||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||||||||||| ||| |||||  ||  || |||        || ||   | | ||   ||   | ||  || | || ||         |  | ||   | |  || | |   | 
GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagagtta-cagactactttttcttcatttcaatgtcacaatcaaacttcattaatttcatgaaaagagaagaactccgacattgacagcttactc

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 10
GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagt----aggattttcatacttagacccgtttatgctattttccttattccagttagtttagttaatttgcttgtcaagaatcttccttgtact--gttcgtt---
|| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    ||||||      || | |  | | ||||  |      |     ||   || | |||  | | ||| | | |  | | |    | |  |  |||| ||  ||   |    
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttaccgagaatatactgcatagattcacg---gtagagttatataatgcag--aatctagatgaatctcctct----atttctttttgtgcttagtaaatctcc

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G00380.1 (Glycine max), 5'ss of exon 10
GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtaggattttcatac-ttagacccgtttatgctattttcct-tattccagttagtttagttaatttgcttgtcaagaatcttccttgtactgttcgtt---
|| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    |||||| |  |    |||   |  ||   || |   ||   |  | || | |||  | | ||| | | |  ||  || |      |  |||    |||   |   
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttgc-tgagaatatactgcacagattcacagtagagttatataatgcag--aatctagatgaat--ctcctctacttctctttttgcttagtttcatgtt

upper sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G00380.2 (Glycine max), 5'ss of exon 10
GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtag----gattttcatacttagacccgtttatgctattttccttattccagttagtttagt-taatttgcttgtcaagaatcttccttgtactgttcgtt
|| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    |||||| |    || | |  | |  |||  |      |   | |    |     |  ||| | | | |  | | ||| ||      |||  ||  |   |||   
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGGTGAgttgctgagaatatactgcacagattcacagtagagttatataatgcagaatctagatgaatctcctctacttctctttttgcttagtttcatgtttcac-

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|32796344|gb|CD948580.1|CD948580
EST:     GATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: GATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|211272295|gb|FL440029.1|FL440029
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTGGATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|149085153|gb|EE174657.2|EE174657
EST:     TTATTTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|211010290|gb|FL457993.1|FL457993
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTGGATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|91868897|gb|EB400200.1|EB400200
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|32808758|gb|CD960992.1|CD960992
EST:     GATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: GATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|32796451|gb|CD948687.1|CD948687
EST:     GATCCGCAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: GATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|32836604|gb|CD976282.1|CD976282
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTGGATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGTTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
EST: gi|148972711|gb|EE023671.2|EE023671
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA                         GTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGA

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), 39 (downstream exon)
Score: 130

GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGAAACTTGTTAATCCTTTCTTGTGGAGGTGCTACTCCATAGCAACGTTCCA


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

GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGAAACTTGTTAATCCTTTCTTGTGGAGGTGCTACTCCATAGCAACGTTCCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 192

GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGAAACTTGTTAATCCTTTCTTGTGGAGGTGCTACTCCATAGCAACGTTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGATGGTTGATGCCGTAGATGCTGTAAGTAATGCGTCAAATACCTTTTGAAACTTGTTAATCCTTTCTTGTGGAGGTGCTACTCCATAGCAACGTTCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagtaggattttcatacttagacccgtttatgctattttccttattccagttagtttagttaatttgcttgtcaagaatcttccttgtactgttcgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC