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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttattattccttaaaagctatatttgccctgattaattcagtgctatttctactgaagactaatttcaccccatctgattcaaccgagatgtgtaccttccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTCTTTGGTGGTTCTCTCGTGCCATACTACTTAGAAGAAGAGGCTAACTGGG

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 5
gtatg-ttattattcctt-----aaaagctatat---ttgccctgattaattcagtgctatttctactgaagactaatttcaccccatctgattcaaccgagatgtgtaccttccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTCTTTGGTGGTTCTCTCGTGCCATACTACTTAGAAGAAGAGGCTAACTGGG
||||| || || ||         ||||   ||||   || | |||||  ||    ||| | ||||||||||||  ||            | |||     ||  | |  | ||||  | ||||||  ||||||||||||| || ||||| ||||||||||||  |||||||||||||||||| ||||| || ||||||||||| |||||||||||||||||| 
gtatggttgttcttgaaagaaaaaaaaaacatatcttttccactgatggatgtgatgccacttctactgaagagcaaa--------ggataatttcgttga--tataaatcttctgtggcagATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTCTTTGGTGGGTCTCTGGTCCCATACTACTTGGAAGAAGAGGCTAACTGGA

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------gtatgttattattccttaaaagctatatttgccctgattaattcagtgctatttctactgaagactaatttcaccccatctgattcaaccgagatgtgtaccttccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTCTTTGGTGGTTCTCTCGTGCCATACTACTTAGAAGAAGAGGCTAACTGGG
                                                       |  || |||     ||      | | ||  | ||| |||   ||  | |  || |  |  | |   ||| |     ||||   |  ||    |  |||   || |     ||||| |||||||||| |||||||| |||||||| || ||||| || || ||||||||||||||||| || ||||| ||  | |||||    || |||||||
gtaatggccttttctaagttggatttgcaagcatgattctccaacaagtttcttcttcgtcatttccttttcttttttctcttatctctggttacaccaagggtgcttgtgttccaaagccattcccatatatcta--ttgactattacctgtgtattgca----agATTTTGGTTCCTGTCCCACAATATCCGCTTTACTCAGCTGCAATATCTCTCTTTGGTGGTTCTCTTGTTCCATATTATCTGGAAGAGACAGCAAACTGGG
















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|29615657|gb|CB620669.1|CB620669
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29671704|gb|CB667979.1|CB667979
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58611970|gb|CK039682.1|CK039682
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGGTGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29614592|gb|CB619605.1|CB619605
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|33799763|gb|CF325747.1|CF325747
EST:     CAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCC-CAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: CAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29684690|gb|CB680965.1|CB680965
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58589507|gb|CF987815.1|CF987815
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29616796|gb|CB621808.1|CB621808
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29645692|gb|CB650699.1|CB650699
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|33381143|gb|CF196486.1|CF196486
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58607278|gb|CK035311.1|CK035311
EST:     AGTGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGACAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AG-GTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|13420574|gb|AU174664.1|AU174664
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29615352|gb|CB620364.1|CB620364
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29615840|gb|CB620852.1|CB620852
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|87005459|gb|CI285681.1|CI285681
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAGTGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58693367|gb|CK082054.1|CK082054
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29676307|gb|CB672582.1|CB672582
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCGCAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|33381689|gb|CF197032.1|CF197032
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29616434|gb|CB621446.1|CB621446
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29614424|gb|CB619437.1|CB619437
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29636374|gb|CB641383.1|CB641383
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58693563|gb|CK082250.1|CK082250
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58687854|gb|CK076541.1|CK076541
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|33381833|gb|CF197176.1|CF197176
EST:     TGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: TGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|58694270|gb|CK082957.1|CK082957
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29614163|gb|CB619176.1|CB619176
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|38477834|gb|CF961967.1|CF961967
EST:     AAGGTGTGATGCAAGTGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|33799684|gb|CF325705.1|CF325705
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
EST: gi|29689279|gb|CB685554.1|CB685554
EST:     AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGG                         ATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTC

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: 69 (upstream exon), 66 (downstream exon)
Score: 211

TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatgttatt ... tccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTCTTTGGTGGTTCTCTCGTGCCATACTACTTAGAAGAAGAGGCTAACTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagactaatttcaccccatctgattcaaccgagatgtgtaccttccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTCTTTGGTGGTTCTCTCGTGCCATACTACTTAGAAGAAGAGGCTAACTGGG
                                        taccttccttc  CT-rich tract
     actaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttattattccttaaaagctatatttgccctgattaattcagtgctatttctactgaagactaatttcaccccatctgattcaaccgagatgtgtaccttccttcgcagATTCTGGTTCCTGTTCCACAATACCCGCTTTATTCTGCTGCCATTTCCCTCTTTGGTGGTTCTCTCGTGCCATACTACTTAGAAGAAGAGGCTAACTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG