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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttctaacaaattcaagataatataccaattgagatccatacagtactgctcactgacatgtgggcccgagggtctgtggggccctctctcataat...

Basic information

species Oryza sativa
transcript LOC_Os08g41460.6
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41460.8 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G885392_T01 (Zea mays), 5'ss of exon 6
ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttctaacaaattcaagataatataccaattgagatccatacagtactgctcactgacatgtgggcccgagggtctgtggggccctctctcataat------
|||||||||  |||||||||| || || ||||| |||||||||||||||||||| |||  |  |||||| ||| |  | |||   |    |||| |    ||  | | ||||| |  ||   | || |  |||   | |      |   ||       
ATTCTTCTTTTTGGATGATTTCACGGGATTTGAAATCACATATCTTCTTGAGgtaagtattgtcaaattgaag-tcttttact--tcactatccttg--ataa-gtttactgaaagttgtttctgatgagctggaagcctggaagttgaaaattgggg

upper sequence: LOC_Os08g41460.8 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G03730.1 (Glycine max), 5'ss of exon 7
ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttctaacaaattcaagata-atataccaattgagatccatacagtac-tgctcactgacatgtgggcccgagggtctgtgg-ggccctctctcataat
 ||||||||||| |||||| |||| || ||||||||||||||||| || |||||  ||||     | || |  ||  || || ||    | |   ||    |   |||    |||    ||      |  |  | ||   |   | |  |||   
GTTCTTCTTCCTTGATGATCTGACTGGATTTGAGATCACATATCTACTAGAGgtatgttcccctcattttatcatgcatctagcatagcaaactgatcgtttggatgcagtttgattcctgaatgtcatagcatctgatagtaattttacat---

upper sequence: LOC_Os08g41460.8 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G14240.1 (Glycine max), 5'ss of exon 7
ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttctaacaaattca------agataatataccaattgagatccatacagtactgctcactgacatgtgggcccgagggtctgtggggccctctctcataat
 ||||||||||| |||||| |||| || ||||||||||||||||| || |||||  ||||     | || |      |  ||  ||| |||    ||||  |    | | |||   |  || |   | |  ||| |||    |    | |  |||   
GTTCTTCTTCCTCGATGATCTGACTGGATTTGAGATCACATATCTGCTAGAGgtatgttcccctcattttatcttgcacctagcatagcaaact-gatcatttggatgcagcttgattcca-gaatgtcataggatctaatagaaatttta-cat---

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|29625905|gb|CB630916.1|CB630916
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         CTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|33684521|gb|CF312760.1|CF312760
EST:     ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|3763529|gb|AU030281.1|AU030281
EST:     GATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: GATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|33682743|gb|CF310982.1|CF310982
EST:     ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|29683116|gb|CB679391.1|CB679391
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|58595312|gb|CF993620.1|CF993620
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         CTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|29684942|gb|CB681217.1|CB681217
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|33681150|gb|CF309389.1|CF309389
EST:     GATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: GATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|33675090|gb|CF303329.1|CF303329
EST:     TCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|88852696|gb|CI008889.1|CI008889
EST:     GTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: GTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|87029164|gb|CI276432.1|CI276432
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|33676087|gb|CF304326.1|CF304326
EST:     ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|29662553|gb|CB658828.1|CB658828
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|29683115|gb|CB679390.1|CB679390
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|25806680|gb|CA762641.1|CA762641
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         CTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|29663222|gb|CB659497.1|CB659497
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|15854892|gb|BI807704.1|BI807704
EST:     CAGGTTTTGGAGATCACATATCTTCTGTGAG                         CTGCCAGA-CCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCT
genomic: CAGGTTTT-GAGATCACATATCTTCT-TGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCT
EST: gi|163920678|gb|EG710011.1|EG710011
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|29615644|gb|CB620656.1|CB620656
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         CTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|33675509|gb|CF303748.1|CF303748
EST:     ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: ATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|86505080|gb|CI147713.1|CI147713
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
EST: gi|88966192|gb|CI013068.1|CI013068
EST:     TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAG                         TTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA
genomic: TCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttcta ... aatgatgcagTTGCCAGAGCCTTTCAGTTTCATCTTCACATGGTTTGCCGCACTGCCTCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTTCTTCCTGGATGATTTGACAGGTTTTGAGATCACATATCTTCTTGAGgttagttctaacaaattcaagataatataccaattgagatccatacagtactgctcactgacatgtgggcccgagggtctgtggggccctctctcataat

- - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - AGATCA