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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggcattgggtcaacattttcagcattggcacttggagccatgtggaagatcatcaccttatttgacattgttcgttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG

Basic information

species Zea mays
transcript GRMZM2G115518_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115518_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g50030.1 (Oryza sativa), 3'ss of exon 10
--------------------------------------------------------------------gtatttggcattgggtcaacattttcagcattggcacttggagccatgtggaaga-----------tcatcacctta--------tttgacattgttcgttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG
                                                                    ||   |   ||||   |||  |    | ||| |    | ||| |||||  ||||            || | ||  ||          ||||     |   | ||   ||||| ||||||| || || || ||||||||||| || |||||||||||||||||||| ||||||||||| |||||||| ||||| ||||||||||| || |
gtatttatgatgatttccatgatcccatctgacaccacagctgccttagttggtagggtaatgtttgtgtggataatattgttgcaatttcactaccatggtttgtgggatccatggagaagtaacattttttctcgtaactataacggttaccctgaccaacctttctctgtacagGAATTAAATCTTGCTCCAACTCATTACTCCATCGTTCAAGACTGGATCAGAAAATCCGATGGCAAGCTAAACTTTCTCGGGTTTACCAAATTTTTACATG
















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|110537607|gb|EE041667.1|EE041667
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAATTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|67016487|gb|CO445236.1|CO445236
EST:     ACTTCGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|76013494|gb|DT940664.1|DT940664
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|76284391|gb|DV023959.1|DV023959
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|32833353|gb|CD973031.1|CD973031
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852739|gb|DY542963.1|DY542963
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|110527857|gb|EE032041.1|EE032041
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852791|gb|DY543015.1|DY543015
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|211096943|gb|FL476438.1|FL476438
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|31357313|gb|CD441670.1|CD441670
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCCCAG                         GNNNNNNNTCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852790|gb|DY543014.1|DY543014
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|211350197|gb|FL470902.1|FL470902
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852812|gb|DY543036.1|DY543036
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852772|gb|DY542996.1|DY542996
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTGCTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|91053581|gb|EB163999.1|EB163999
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|24769079|gb|CA404208.1|CA404208
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|24934264|gb|CA452482.1|CA452482
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|78104805|gb|DV523223.1|DV523223
EST:     ACTTCGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|149111454|gb|EE294957.2|EE294957
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852741|gb|DY542965.1|DY542965
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852730|gb|DY542954.1|DY542954
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACGTTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|6626368|gb|AW257900.1|AW257900
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATT
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATT
EST: gi|88852715|gb|DY542939.1|DY542939
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCAACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|33100164|gb|CF060124.1|CF060124
EST:     TTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: TTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|60357690|gb|DN224663.1|DN224663
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|32833934|gb|CD973612.1|CD973612
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
EST: gi|88852722|gb|DY542946.1|DY542946
EST:     ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAG                         GAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA
genomic: ACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGA

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: 79

GCTGGAAGCTTTGGAAAGGTGGGAAGAAATTGCTGGAACAGCTTTTCAGCACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 124

GCTGGAAGCTTTGGAAAGGTGGGAAGAAATTGCTGGAACAGCTTTTCAGCACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 239

GCTGGAAGCTTTGGAAAGGTGGGAAGAAATTGCTGGAACAGCTTTTCAGCACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 118

GCTGGAAGCTTTGGAAAGGTGGGAAGAAATTGCTGGAACAGCTTTTCAGCACTTTGAACAAGAGGGCAACCGAGTTATATCAGTTGAGGAGTTAGCACAGgtatttggca ... ttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttggagccatgtggaagatcatcaccttatttgacattgttcgttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG
                              atttgac  putative branch site (score: 118)
                            ttatttga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttggcattgggtcaacattttcagcattggcacttggagccatgtggaagatcatcaccttatttgacattgttcgttgtgcgtagGAACTAAATCTCGCGCCGACACATTACTCCATTGTGCAAGACTGGATCAGAAAATCGGATGGCAAGCTTAACTTTCTTGGGTTCACCAAATTTTTGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT