Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTCCATTTCAGCTGAAATATTGGACTCGCCCTAAAGACCATCATTATGACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcatttggaatggaacagtcatcaatgcttaagaacaaaaaaaagctattcctaggttgctgagcaaaattgttttaatattttattttatggggtctactatctag

Basic information

species Oryza sativa
transcript LOC_Os03g13540.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13540.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G152477_T01 (Zea mays), 5'ss of exon 4
AACTCCATTTCAGCTGAAATATTGGACTCGCCCTAAAGACCATCATTATGACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcatttggaatggaaca-------gtcatcaatgcttaagaacaaaaaaaagctattcctaggttgctgagcaa-aattgttttaatattttattttatgg-ggtctactatctag--------------
 || || ||||| || || || ||||||| |||||| ||| |||| || ||||||||||| ||||| |||||  |||| |||||||  ||||| || ||||||||  | ||   | ||| |       |||| | |  |         || || ||||||   ||       |||| |   || ||| |||  ||  |||| | | ||  ||  ||||                
CACCCCGTTTCAACTCAAGTACTGGACTCACCCTAAGGACGATCACTACGACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtatgttctcgaatatgagctcgtcagcgagacagcgacgacaagaagagctatgattattggagggagctatggttatttaaatccttctttttgtcgtggattatcatctgcaatattcaattcag
















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|27576382|gb|CA999076.1|CA999076
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|27576775|gb|CA999469.1|CA999469
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|58685580|gb|CK074267.1|CK074267
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGA
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGA
EST: gi|86481343|gb|CI123976.1|CI123976
EST:     ACTGGAGAGGAGTGGCACCTCGACTAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|8527438|gb|AU092253.1|AU092253
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|117234872|gb|CT847928.1|CT847928
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|27577370|gb|CB000065.1|CB000065
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|33660753|gb|CF291720.1|CF291720
EST:     CACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: CACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
EST: gi|58592688|gb|CF990996.1|CF990996
EST:     ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAG                         GATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT
genomic: ACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTT

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: 74 (upstream exon), 73 (downstream exon)
Score: 117

AACTCCATTTCAGCTGAAATATTGGACTCGCCCTAAAGACCATCATTATGACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcattt ... tactatctagGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTCCATTTCAGCTGAAATATTGGACTCGCCCTAAAGACCATCATTATGACTGGAGAGGAGTGGCACCTCGACAAAAATACATAACTAATCTACTTAAGgtgcgcatttggaatggaacagtcatcaatgcttaagaacaaaaaaaagctattcctaggttgctgagcaaaattgttttaatattttattttatggggtctactatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG