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

AATGTTTGTCAGCTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattcttttctaccacctattacatttgatgctagtcagtcgtctgaatggaatcgattattgttgtatgtataacctgttgaactgaatctagag...

Basic information

species Oryza sativa
transcript LOC_Os02g57250.2
intron # 4
splice site 5'
intron type U2

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|3760881|gb|C98135.1|C98135
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86535627|gb|CI175833.1|CI175833
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTT-AACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|89170905|gb|CI040182.1|CI040182
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86850814|gb|CI338790.1|CI338790
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88838170|gb|CI372738.1|CI372738
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAAGAACCATTGCTTCAACAAGAGGCAAG
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCAC-AGAACCATTGCTTCAACAAGAGGC-AG
EST: gi|14571418|gb|BI118786.1|BI118786
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCCGATACCAGTGAATTCACAGAACCATTGCTTCAACAAGAGGGCAG
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGC-GATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGG-CAG
EST: gi|88286689|gb|CI517800.1|CI517800
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGTTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88252911|gb|CI350336.1|CI350336
EST:     CTCTTTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGGCTTCAACAAGAGGCAGA
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATT-GCTTCAACAAGAGGCAGA
EST: gi|88466011|gb|CI519884.1|CI519884
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86835880|gb|CI346077.1|CI346077
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|58688338|gb|CK077025.1|CK077025
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|58683213|gb|CK071900.1|CK071900
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|13165375|gb|AU174172.1|AU174172
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTNTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86863834|gb|CI332845.1|CI332845
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86510796|gb|CI153429.1|CI153429
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86904641|gb|CI321549.1|CI321549
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGCCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|313079501|gb|HO213059.1|HO213059
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86873635|gb|CI330013.1|CI330013
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88274579|gb|CI394985.1|CI394985
EST:     AGAGGGTGA-GATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCACAT
genomic: AGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|89176834|gb|CI013407.1|CI013407
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88963014|gb|CI025500.1|CI025500
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|55409064|gb|CV721440.1|CV721440
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88319682|gb|CI520725.1|CI520725
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGTTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|87034650|gb|CI189274.1|CI189274
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|29645716|gb|CB650723.1|CB650723
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86842406|gb|CI335293.1|CI335293
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|89194933|gb|CI003397.1|CI003397
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88263818|gb|CI367592.1|CI367592
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|5456482|gb|AU075793.1|AU075793
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86879087|gb|CI315459.1|CI315459
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGTACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|86545878|gb|CI186084.1|CI186084
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|3761036|gb|C98290.1|C98290
EST:     GGTTGAGGATCATGAGGNCATCCAGATGCCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTNCAACAAGAGGCAGA
genomic: GGTTGAGGATCATGAGGACAT-CAGATG-CGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTT-CAACAAGAGGCAGA
EST: gi|29685040|gb|CB681315.1|CB681315
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88979064|gb|CI025572.1|CI025572
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|89198698|gb|CI003435.1|CI003435
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|88465390|gb|CI529610.1|CI529610
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCANCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
EST: gi|287065|gb|D15870.1|D15870
EST:     CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTG                         GTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT
genomic: CTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGAT

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: 71 (upstream exon), 37 (downstream exon)
Score: 3

AATGTTTGTCAGCTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattct ... tccgttgcagGTCAGCGATACCAGGGAATTCACAGAACCATTGCTTCAACAAGAGGCAGATCCTGAGAGCGTGTGACAAGGAAAAGAGCTATACCGCTGGTGAAGCTTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGTTTGTCAGCTCTGTGAAGAGGTTGAGGATCATGAGGACATCAGATGCGAATGGTCTTGgttagattcttttctaccacctattacatttgatgctagtcagtcgtctgaatggaatcgattattgttgtatgtataacctgttgaactgaatctagag

- - - - - - - -  TGAAGA
- - - - - - - - -  AAGAGG
- - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - CAGATG