Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttgccacaacaatttgggaagacaactgttcttgattataagtccttatattttttacctaaccatcttgcag

Basic information

species Zea mays
transcript GRMZM2G092129_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g22640.4 (Oryza sativa), 5'ss of exon 5
TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgtt-------ttctttgc----cacaacaatttg-------ggaagacaactgttcttgattataagtccttatatt-ttttacctaaccatcttgcag
||| ||||| |||||||| |||||||||||| | |||||||||||| |||||||||||||||| |||||||||||||| ||||||||||| || |||||||||       |||||||       ||   |||          ||||  ||    ||||||  |  |||| | ||||  | ||  | ||||||||  |||
TCAGCCAGGCCAAATCATAATGGATATAGATCTTCGTTGGGGTGGTGATCCAAGCATAATCCTTGCTGTTGATGCTGTTGTTGCATCACTTCCTATTCAGgttttactatttctttgttcttttcagtgattaattcttacagaagtaaatctctcttga--actagtcatgatatcatctttgccaaccatctcacag

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G45720.1 (Glycine max), 5'ss of exon 5
TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttgccacaacaatttggga--agacaactgttcttgattataagtccttatattttttacc-taaccatcttgcag----
| |   |||||||||||| ||||| || |||||||||||||||||| |||| |  ||  |  | |||||||| ||  | ||||| ||| | || |||||||||    |  |||      ||         |   |   |    || | || |  | ||| |||  |     |   | ||        
TAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGTTGCGTCAATCCCTATTCAGgttagactcaccagtgtttttcaatgttgaatttcacattcctataagaatttttcataatttggagtgctattgttttttgctcag

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G02370.2 (Glycine max), 5'ss of exon 5
TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTA---GTTGCATCACTGCCAATTCAGgttttctttgccacaacaat--ttgggaagacaactgttcttgattataagtcct--tatatttttt--acctaaccatcttgcag----------------------------------------------------------------
 |||  |||||||||||| |||||||| |||||||||||||||||| |||| || || ||  | |||||||| |||| |   ||||||||| | || || |||||     ||  |  ||  ||  ||      |   || || |     || | ||||  | |   | ||  | ||   | | |||||                                                                 
-CAA--AGGTCAAATCATAATGGATATTGATTTCCGTTGGGGTGGTGATCCTAGTATTATTTTGGCTGTTGAAGCTGCACTTGTTGCATCAATCCCTATACAGgtaagacttaaccgaatcataatttcatcaatccctattttgttgcatcattcctattgtggctgttgaagctgctcttgttgcatcataatttcgtcacattccttttacaatttgtaaaaactgaagttttattgaattttgtttcag

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA07G09070.1 (Glycine max), 5'ss of exon 6
TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTA---GTTGCATCACTGCCAATTCAGgttttctttgccacaacaat--ttgggaagacaactgttcttgattataagtccttatatttttt--acctaaccatcttgcag----------------------------------------------------------------
 |||  |||||||||||| |||||||| |||||||||||||||||| |||| || || ||  | |||||||| |||| |   ||||||||| | || ||||||||     ||  |  ||  ||  ||      |   || || |     || |  || |     | ||  | ||   | | |||||                                                                 
-CAA--AGGTCAAATCATAATGGATATTGATTTCCGTTGGGGTGGTGATCCTAGTATTATTTTGGCTGTTGAAGCTGCACTTGTTGCATCAATCCCTATTCAGgtaagacttagctgaatcataatttcatcaatccctattttgttgcatcaacccattgggctgttgaagctgcacttgttgcatcataattttgtgacattcctttcacaaattttaaaaattgaagttttattgtcttttctttcag

upper sequence: GRMZM2G092129_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA09G40290.1 (Glycine max), 5'ss of exon 6
TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttgccacaacaatt---tgggaagacaactgttcttgattataagtccttatattttttacctaaccatcttgcag-----
| |   |||||||||||| ||||| || |||||||||||||||||| |||| |  ||  |  | |||||||| ||  | ||||||||| | || |||||||||    |  |||      ||   ||   |    ||  | ||  |  | |  |    | |||||     | |    |||         
TAACAAAGGTCAAATCATAATGGACATTGATTTCCGTTGGGGTGGTGATCCCAATATTGTTTTGGCTGTTGAAGCACTTGTTGCATCAATCCCTATTCAGgttagactcaccagtgtttttccatgttgaattcacattcctataggaaatttttcaaaattttgagtgttattggcttttgcttcag

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|148971559|gb|EE022272.2|EE022272
EST:     CAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAG                         CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCT
genomic: CAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCT
EST: gi|211220820|gb|FL457379.1|FL457379
EST:     GTAGTTGCATCACTGCCAATTCAG                         CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCT
genomic: GTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCT
EST: gi|71331353|gb|DR802511.1|DR802511
EST:     CAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAG                         CTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCT
genomic: CAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCT

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), 46 (downstream exon)
Score: 164

TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 163

TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 155

TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttg ... catcttgcagCTCAAGGATCTTCAGGTCTATACTGTCATACGTGTTATATTTCAACTGTCTGAAGACATCCCTTGCATTTCTGCTGTTGTTGTGGCTCTCCTTGCTGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACCAGGTCAAATCATCATGGATATAGATTTCCGTTGGGGTGGTAATCCAAGCATAATCCTAGCTGTTGATGCTGTAGTTGCATCACTGCCAATTCAGgttttctttgccacaacaatttgggaagacaactgttcttgattataagtccttatattttttacctaaccatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG