Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacactcacacagtacaatcttccttccatcataccatccgtatattctgctgagaccgcaattgatgtctacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTCGTTGCGCTTTTTCTGCTGGTATACTACTTGACCAGGTAGAAGAGGACCA

Basic information

species Oryza sativa
transcript LOC_Os02g57510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57510.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G101571_T02 (Zea mays), 3'ss of exon 5
gtaaacactcacacagtacaatcttccttccatcataccatccgtatattctgctgagaccgcaattgatgtctacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTCGTTGCGCTTTTTCTGCTGGTATACTACTTGACCAGGTAGAAGAG--GACCA
|||| |    | | |  |||||     |   |  |  ||    ||     || ||||||     ||  ||||      |  |||| ||||||||||||||||| |||||||||||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||||||||   |||  
gtaagcgacaagagaa-acaattaaatt---agtaggccgattgtgc--ccttctgaga---tgatccatgt-----gtgcagGTATTTGAGACCAAATCAAGCCGGAGGATGGGAACCCTCGTCGCATCATTCGTCGCCCTTTTTCTGCTGGTTTACTACTTGACCAGGTAGAAGACATGAC--

upper sequence: LOC_Os02g57510.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0051g00940.t01 (Vitis vinifera), 3'ss of exon 5
------------gtaaacactcacaca-----gtacaatcttccttccatcataccatccgtatattctgctgagaccgcaattgatgtctacgatat----agGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTCGTTGCGCTTTTTCTGCTGGTATACTACTTGACCAGGTAGAAGAGGACCA
            |  |||    |   |     |||  || || ||| |   | | ||| | | |  |   ||| |  |   ||  || | |  ||| |    |||| ||||||||||||||||| |||||||||   || ||  | ||||| || || |   |||| ||  |  |||||||| |||| ||||| | ||    | 
gtaagtagactagataacctctatctattggtgtaatattttgctttctcgaaaacatgctttttcttgactggg--catgatgaatatgtttgatctgactagGTGTTTGAGACCAAATCAAGCCGGAGGATGTTTACGCTTATTGCATCGTTTGTGGTCATTTTCCTAGTCATATACTACCTGACTAGGTAAATGATACACT
















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|88844227|gb|CI005600.1|CI005600
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|87033084|gb|CI187708.1|CI187708
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88225322|gb|CI225238.1|CI225238
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86889782|gb|CI333433.1|CI333433
EST:     TCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86252809|gb|CI010291.1|CI010291
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88240546|gb|CI239708.1|CI239708
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86259248|gb|CI010549.1|CI010549
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|29677589|gb|CB673864.1|CB673864
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88266777|gb|CI377679.1|CI377679
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86594404|gb|CI251276.1|CI251276
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|89189000|gb|CI012150.1|CI012150
EST:     AGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: AGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88206344|gb|CI206193.1|CI206193
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88847279|gb|CI011222.1|CI011222
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88829868|gb|CI004906.1|CI004906
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|89163094|gb|CI099984.1|CI099984
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86501990|gb|CI144623.1|CI144623
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86870285|gb|CI319391.1|CI319391
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86252311|gb|CI056048.1|CI056048
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88844063|gb|CI001120.1|CI001120
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88970621|gb|CI385311.1|CI385311
EST:     ATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGAC-AGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: ATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|218494842|gb|FG955901.1|FG955901
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|58690451|gb|CK079138.1|CK079138
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88835244|gb|CI370547.1|CI370547
EST:     GTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         NTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: GTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86853121|gb|CI324823.1|CI324823
EST:     CTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGAT-GGAACCCTCGTAGCATCATTC
genomic: CTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88980662|gb|CI022375.1|CI022375
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|58672890|gb|CK061576.1|CK061576
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88966184|gb|CI013060.1|CI013060
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|163918361|gb|EG714041.1|EG714041
EST:     GTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: GTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88202410|gb|CI201272.1|CI201272
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88832609|gb|CI008205.1|CI008205
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|88902951|gb|CI088489.1|CI088489
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|89197729|gb|CI013719.1|CI013719
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|86416944|gb|CI030955.1|CI030955
EST:     GGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: GGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
EST: gi|89180748|gb|CI009656.1|CI009656
EST:     TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATG                         GTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC
genomic: TGGATTCGTCAAGGGGTTTTCTGTCTGGAACAGTGGACAAGTTCAAGATGgtaaacactc ... tacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatcataccatccgtatattctgctgagaccgcaattgatgtctacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTCGTTGCGCTTTTTCTGCTGGTATACTACTTGACCAGGTAGAAGAGGACCA
                                   aattgat  putative branch site (score: 4)
                tatattct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacactcacacagtacaatcttccttccatcataccatccgtatattctgctgagaccgcaattgatgtctacgatatagGTTTTTGAGACCAAATCAAGTCGGAGGATGGGAACCCTCGTAGCATCATTCGTTGCGCTTTTTCTGCTGGTATACTACTTGACCAGGTAGAAGAGGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA