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

TGGGACCGTATGCCTGTCGCTTTACTCATTGGTTGCCGGAATTTTTGGTATGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaaccattacaaaagggtcgtttaccgtcaataaattgtggcctgtctaaccaagctgtaaactttgttcctgcgtcacag

Basic information

species Oryza sativa
transcript LOC_Os03g53110.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G159295_T01 (Zea mays), 5'ss of exon 10
TGGGACCGTATGCCTGTCGCTTTACTCATTGGTTGCCGGAATTTTTGGTATGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaaccattacaaaagggtcgtttaccgtcaataaattgtggcctgtctaaccaagctgta-aactttgttcctgcgtcacag
||| ||||| || |||||||| |||||||| ||||| ||| | ||||||||||| ||||| || ||||||||||||  ||| |||||| | |||||||||||| ||      |  |||           ||    |||| | ||  || |  ||        |||  |||||  | |   | ||||||
TGGTACCGTCTGTCTGTCGCTGTACTCATTAGTTGCTGGAGTCTTTGGTATGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttctgctcgcaa----------cacgacaaatataatgatgcgttgct-------ttgtgtaacttgatcctcccttcacag

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G159295_T02 (Zea mays), 5'ss of exon 10
TGGGACCGTATGCCTGTCGCTTTACTCATTGGTTGCCGGAATTTTTGGTATGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaaccattacaaaagggtcgtt-taccgtcaataaattgtggcctgtctaa-ccaagctgtaaactttgttcctgcgtcacag
||| ||||| || |||||||| |||||||| ||||| ||| | ||||||||||| ||||| || ||||||||||||  ||| |||||| | |||||||||||| ||      |  ||| | |     | ||  |         | ||       | | ||   ||  | |  | |||| ||  |||   
TGGTACCGTCTGTCTGTCGCTGTACTCATTAGTTGCTGGAGTCTTTGGTATGAATATTCCGTATACCTGGAATGACGGCCACGGATACATCTTCAAATGGgtaggtttctgctcgcaacacgacaaatataatgatgcgttgctttgtgtaacttgatcctcccttcacaggtggttcttgtatcag--

upper sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 5'ss of exon 11
TGGGACCGTATGCCTGTCGCTTTACTCATTGGTTGCCGGAATTTTTGGTATGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaaccattacaaaagggtcgtttaccgtcaataaattgtggcctgtcta-accaagctgtaaactttg---ttcctg--cgtcacag
||| || || ||| | ||| | |||||  | || || |||||||| || ||||||||||||||||| ||||| |||   ||||||||| | |||||||  |||||  |||||  |    |   |||  |   |   | | |  |    || || | |  ||  | |     | |   ||  ||   ||  |||
TGGAACAGTTTGCTTATCGATGTACTCTCTTGTCGCTGGAATTTTCGGGATGAACATTCCATACACATGGAACGACGGTCATGGATACATGTTCAAATACgtaaga-aaccagaattcta--ttcgcatgaggatgaaataaagatctctctcaagattaacttatgtttatcggggtttttggttgttgcag

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|86491085|gb|CI133718.1|CI133718
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|3763402|gb|AU030154.1|AU030154
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88845073|gb|CI083998.1|CI083998
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|38468461|gb|CF952592.1|CF952592
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|89181743|gb|CI113249.1|CI113249
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88456911|gb|CI529112.1|CI529112
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|86495286|gb|CI137919.1|CI137919
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|86496775|gb|CI139408.1|CI139408
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|27547079|gb|CA767318.2|CA767318
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88429897|gb|CI562708.1|CI562708
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88413290|gb|CI523851.1|CI523851
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTNTCAGGACTTTTCTGTGCCTTCATGTTCTTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88840990|gb|CI000952.1|CI000952
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGCTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88476382|gb|CI413653.1|CI413653
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTGTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|86874289|gb|CI335901.1|CI335901
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|313083966|gb|HO213749.1|HO213749
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|89178025|gb|CI391204.1|CI391204
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|86252029|gb|CI055766.1|CI055766
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88963590|gb|CI029384.1|CI029384
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88442581|gb|CI544148.1|CI544148
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|58683065|gb|CK071752.1|CK071752
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88448280|gb|CI555135.1|CI555135
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTNTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
EST: gi|88461422|gb|CI526930.1|CI526930
EST:     TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGG                         GTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT
genomic: TGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTT

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 1 RNA-Seqlibrary.


Block sizes: 30 (upstream exon), 75 (downstream exon)
Score: 10

TGGGACCGTATGCCTGTCGCTTTACTCATTGGTTGCCGGAATTTTTGGTATGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaac ... tgcgtcacagGTGGTTCTCGTGTCAGGACTTTTCTGTGCCTTCATGTTCGTCTCCATTGTTGCGTACGCACGGCACAAGGGCCTCGTCGGGTCGTGAACCTTGCCCAAAC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGACCGTATGCCTGTCGCTTTACTCATTGGTTGCCGGAATTTTTGGTATGAACATTCCATACACCTGGAATGACAACCATGGATACGTATTCAAATGGgtaagtcaaccattacaaaagggtcgtttaccgtcaataaattgtggcctgtctaaccaagctgtaaactttgttcctgcgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA