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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaaattatgaaaaatgctttactttgatcctttatccttctatattttagaatgaaatatgcacctatttactgttttgtggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTT

Basic information

species Oryza sativa
transcript LOC_Os02g43930.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 3
gtaataaaattat---gaaaaatgctttactttgatcctttatcctt-ctatattttagaatgaaata-tgcacc---tatttactgttttgtggttgaaagTAGGTAG------AGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTT
||||| ||| |||   |     |  ||||  |  ||| ||  | | | ||    ||| || | ||||| | |||    ||||||  | ||| ||||| | ||  |||||      ||||| ||||||||||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| ||||| || ||||| |||||      
gtaatcaaaatatcttgtggtgttgtttatatatatcgttgcttcatgcttccctttggattaaaatactacactggttatttatcggtttatggttaatagGTGGTAGCTCAAGAGGACGCAGACAAAAGCGTGGTGAAGATGTGGTGCATACTATGAAGGTTTCCTTAGACGATCTGTACAATGGGACAACCAAGAAACT------

upper sequence: LOC_Os02g43930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------gtaataaaattatgaaaaatgctttactttgatcctttatccttctatattttagaatgaaatatgcacctatttactg--------ttttgtggttgaaagTAGGT--AGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTT
                                 || | |  || | |||  ||   |  |||  |   |     |     | |||  ||| | ||||  ||  |||  |          |||||| | ||   |||| |  ||||||   || || || || || |||||||| || |||||| ||||||||||||| || ||| |||||||||| || | |||| ||        
gtaagaggatgcttacttaaatttcttgatctttatttattttttcaaatgtgtacttatttcctgtctacctttaaagaaattttcaattatatatttactgattcccaagtatctaattttgtagGTGGTGGTAGCTCAAGAGGAAGAAGGCAGAAACGAGGTGAAGATGTTGTGCATACTTTGAAGGTTTCTTTGGAGGACTTGTATAATGGCAC-ATCAAAGAA--------
















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|33797209|gb|CF324468.1|CF324468
EST:     TATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|27576325|gb|CA999019.1|CA999019
EST:     ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58661241|gb|CK049921.1|CK049921
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58672684|gb|CK061370.1|CK061370
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|33796281|gb|CF324007.1|CF324007
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|29631437|gb|CB636446.1|CB636446
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCG
EST: gi|58677822|gb|CK066509.1|CK066509
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58663897|gb|CK052583.1|CK052583
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58664824|gb|CK053510.1|CK053510
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAAGCGTGGCGAAGATGTGGTACATACTATG
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAA-GCGTGGCGAAGATGTGGTACATACTATG
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58666150|gb|CK054836.1|CK054836
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|13420811|gb|AU174901.1|AU174901
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58601753|gb|CK012281.1|CK012281
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|29673001|gb|CB669276.1|CB669276
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|218492553|gb|FG956401.1|FG956401
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         TAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58601372|gb|CK011900.1|CK011900
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|27577056|gb|CA999750.1|CA999750
EST:     ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTT-GGG                         --GGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: ATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58658625|gb|CK047305.1|CK047305
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
EST: gi|58589635|gb|CF987943.1|CF987943
EST:     TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGG                         --G-TAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA
genomic: TCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGA

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: 67 (upstream exon), 34 (downstream exon)
Score: 3

GATGCACTCAAAGAAGGAATGGGAGGAGGCAGCAGCAGTGATTTCCATAGTCCCTTCGATTTATTTGAGCAAATTTTTCAGAATCGTGGTGGCTTTGGGGgtaataaaat ... tggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttctatattttagaatgaaatatgcacctatttactgttttgtggttgaaagTAGGTAGAGGACACAGACAAAAGCGTGGCGAAGATGTGGTACATACTATGAAGGTTTCTTTAGAAGACCTGTATAATGGTACTACCAAAAAACTGTCTTT
      tatattttagaatgaa  TA-rich tract