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

GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacag

Basic information

species Oryza sativa
transcript LOC_Os05g06430.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G110742_T02 (Zea mays), 5'ss of exon 10
GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccat--gcttcatcatatgacag-----------
| | |||||||| |||||||   ||||||||||||||||||| ||||||||||| ||||||||||||||  ||||||||||||| |||||| ||||||||||| |||  | ||||||| || |||| ||||| | |       |||||||| | |  |||| || ||||||||  | ||| |  |     ||           
GCATGGAAAGATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAGgtgggca-tataagtttccat-cctccattcaatctttgagctatattact-atttaagaagctaatttccataagtttcttagtggtgtagctagttcagta

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G008647_T02 (Zea mays), 5'ss of exon 7
GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacag
| | ||||| || |||||||   ||||||||||||||||||| ||||||||||| ||||||||||||||  ||||||||||||| |||||| ||||||||||| |||  | ||||||| || |||| ||||| | |       |||||||| | |  |||| || ||||||||   |  || ||      
GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAGgtgggca-tataagtttccat-cctccattcaatctttgagctatattact-atttaagaagctaatttccataagtt-tcttag-----

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G159369_T01 (Zea mays), 5'ss of exon 10
GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacag
| | |||||||| |||||||   |||||||||||||||| || ||||||||||| ||||||||||||||  ||||||||||||| |||||| ||||||||||| |||  | ||||||| || |||| ||||| | |       |||||||| | |  |||| || ||||||||  || ||  |||   ||
GCATGGAAAGATATATGTGACAGCTGCAAAGAAGATCATAGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAGgtgggca-tataagtttccat-cctccattcaatctttgagctatattact-atttaagaagctaatttccatattttattgtattgtag

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G138616_T01 (Zea mays), 5'ss of exon 3
GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccat--gcttcatcatatgacag-----------
| | |||||||| |||||||   ||||||||||||||||||| ||||||||||| ||||||||||||||  ||||||||||||| |||||| ||||||||||| |||  | ||||||| || |||| ||||| | |       |||||||| | |  |||| || |||| |||  | ||| |  |     ||           
GCATGGAAAGATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAGgtgggca-tataagtttccat-cctccattcaatctttgagctatattact-atttaagaagctaattttcataagtttcttagtggtgtagctagttcagta

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G008647_T04 (Zea mays), 5'ss of exon 3
GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccat--gcttcatcatatgacag-----------
| | ||||| || |||||||   ||||||||||||||||||| ||||||||||| ||||||||||||||  ||||||||||||| |||||| ||||||||||| |||  | ||||||| || |||| ||||| | |       |||||||| | |  |||| || ||||||||  | ||| |  |     ||           
GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAGgtgggca-tataagtttccat-cctccattcaatctttgagctatattact-atttaagaagctaatttccataagtttcttagtggtgtagctagttcagta

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|163925853|gb|EG714953.1|EG714953
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|3768455|gb|AU032482.1|AU032482
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|58672427|gb|CK061113.1|CK061113
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|33803520|gb|CF327635.1|CF327635
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|2799505|gb|AA752494.1|AA752494
EST:     CTAAGAAGGAATCTGAGAGGCTTCAACGCATGTNGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|11026410|gb|AU163011.1|AU163011
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|86482186|gb|CI124819.1|CI124819
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|88248551|gb|CI248400.1|CI248400
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|86513133|gb|CI155766.1|CI155766
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|87017864|gb|CI273886.1|CI273886
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     CTGAATACACTAAGAAGGAATCTGAGAAGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTC
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTC
EST: gi|5003011|gb|AU068120.1|AU068120
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|58683615|gb|CK072302.1|CK072302
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|33803570|gb|CF327660.1|CF327660
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
EST: gi|86593482|gb|CI264361.1|CI264361
EST:     CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG                         TCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT
genomic: CTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaaca ... catatgacagTCGATCAGTCCTTCCAAAGCCGATGAATTCGTCATCAAGAAGAACATCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAGgtgagcaacaaaagtttctattcctcaattcactttggacatcatattacttaatctagaatctgatttccatgcttcatcatatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA