RetrogeneDB ID: retro_cfam_1008

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:16651678..16653324(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NOC3L
• Ensembl ID: ENSCAFG00000008033
• Aliases: None
• Description: nucleolar complex associated 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24034]

Sequence

>retro_cfam_1008
AGAAGAAATAAAAAACAGATCCTAAGCTTTTGGAAGTTTCTAAAGACTAGTAAAGTCAGACTTGAAAACAAGTTGAAAAA
TAAGCAATTTAAACCACAAAGCACTGTCTAGAAGTACTGAAAAGAACAGAGGAAACTAAGGCAGCTGTAAAGGATGTTGT
GTCTAAGAAACCGATCCCACTGGAGGACCTGAAGGAGAAAAGACCAGGTAAAAGAATTGAGAGGGAAGAGGAGGAAGAAG
AGGAAGCACTTCCTTTGGATATGATGAATGAAGATGACTTGCAGTTAATGATAGAGTTAGGACAAAGAGCCTCTTTTCTA
ACGAGAGATCTTTCTTCTAGCGAACCTGTTCACTCCAAGAAACGAAAGCATGAGCATGTTATAGATAAATATGAAAAAAT
ACCAAGAACTCTGCAAACTGCACCAGAGAAGGAACTGATTCACTTGCTTCCCATCAAGGATAAAAGTGGTATAATCCCAC
AGACCAGGGAGAAGCAAGTTACTGACAATAACCAAGATGAAGAGGATCAAGAAGAGGTGGAACTTGAGGAAGAGATTGTT
GAAGATCCCATTCGAGAACTGACATTAGAAGAACATGTAATTGAAAGAAGGAAGAAGCTATAGGATAAGAAAATGCATAT
TGCAGCTTTGGCATCTGCCATATTATCAGATCCAGAAACTAATATTAAAAAATTGAAAGAACTACGTTCTATGCTGATGG
AACAGGATCCTGATGTGGCTGTTACTGTTCAAAAGCTGGTGATAGTTTCCCTGATGGAGTTATTTAAAGACATTACTCCT
TCATATAAAATACAACCCCTCAGAAGAAGAAAAATCCACCAAGATCCTCAAAGAAACCCCCAAATTAAGAGAATTTGAAG
AAGGCCTGGTTAGCCAATGTAAATTTTATTTGGAAAATATGGAGCAAATGATTAAAGACTAGAAGCAAAGGAAACTGAAG
AAAAGTAATGTATTTTCCTTAAAGGCCTACAAAGGACTGGCGGAAGTGGCTGTGAAGAGCCTGTGTGAGCTGTTGGTGTC
ACTACCTCATTTCAACTTTCACAACAACATCATTGTATTGATTGTCCCTCTCATGAATGATGTATCAAAGTCGATCTCTG
GAATGTGTTGTGAGGCAGTAAAGAAATGGTTTAAGCAAGATAAATTAGGCCAAGCTTCCCATGGTGTGATTAAAGTGATT
TCTGGTTTTGTGAAGGGCAGAAATTATGAAGTTAGGTCAGAGATGTTAAAGACATTATTGTGCTTAAGAAATCAGGAAGT
AGAAGTGAAAAAAGATACAGAGGACATTAATAAACCAAAAAAGTTCATGACTTTCAAGGAAAAGAGAAAAACTATCAAGA
ATGCAGAAAAAGTGGAATAAAGCAGAAGAGAAACTAGAGCGAGAGCTTCTGGAGGCAGAAGCTTCAGAGAACACAGAGAG
AAAACTTAAACTGCACATGGAGACTCTGAATATTGTGTTTGTAACCTACTTCAGAATATTGAAGAAGGCCCAGAGTGTAA
CCTCTCCTGCCAGCAGTTCTAGAAGGCCTTGCCAAGTTGGCTTATCTTATAAAAGTGGAGTTTTTTGATGATTTATTAGT
AGTACTTCATACTCTCATTGAGTCTGGTGATCTAAGCTATGGAGAA

Alignment

ORF - retro_cfam_1008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 68.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RRNKKQIPSFRKLLKTSKVKLENKLKNKQFKQQSTLKKYRKEQRKLRQ-AVKDAVSKKPIPLEDPKEKRP
          RRNKKQI.SF.K.LKTSKV.LENKLKNKQFK.QST..KY.KEQRKLRQ.AVKD.VSKKPIPLED.KEKRP
Retrocopy RRNKKQILSFWKFLKTSKVRLENKLKNKQFKPQSTV*KY*KEQRKLRQ<AVKDVVSKKPIPLEDLKEKRP

Parental  GKRIEREEEEEEEALPLDMMDEDDLQLMRELGQRASFLTRDLSSSEPVHAKKRKYERVIDKYEKIPRTLQ
          GKRIEREEEEEEEALPLDMM.EDDLQLM.ELGQRASFLTRDLSSSEPVH.KKRK.E.VIDKYEKIPRTLQ
Retrocopy GKRIEREEEEEEEALPLDMMNEDDLQLMIELGQRASFLTRDLSSSEPVHSKKRKHEHVIDKYEKIPRTLQ

Parental  TAPEKEMIHLLPIKDKSGIIPQTREKPVIDNNQDEEDQEEVELEEEIVEDPIRELTLEEHLIERRKKLQE
          TAPEKE.IHLLPIKDKSGIIPQTREK.V.DNNQDEEDQEEVELEEEIVEDPIRELTLEEH.IERRKKL..
Retrocopy TAPEKELIHLLPIKDKSGIIPQTREKQVTDNNQDEEDQEEVELEEEIVEDPIRELTLEEHVIERRKKL*D

Parental  KKMHIATLASAILSDPETNIKKLKELRSMLMEQDPDVAVTVRKLVIVSLMELFKDITPSY-KIRPLTEAE
          KKMHIA.LASAILSDPETNIKKLKELRSMLMEQDPDVAVTV.KLVIVSLMELFKDITPSY.K..P..E.E
Retrocopy KKMHIAALASAILSDPETNIKKLKELRSMLMEQDPDVAVTVQKLVIVSLMELFKDITPSY>KYNP-SEEE

Parental  KSTKIRKETQKLREFEEGLVSQYKFYLENLEQMVKDWKQRKLKKSNVVSLKAYKGLAEVAVKSLCELLVS
          KSTKI.KET.KLREFEEGLVSQ.KFYLEN.EQM.KD.KQRKLKKSNV.SLKAYKGLAEVAVKSLCELLVS
Retrocopy KSTKILKETPKLREFEEGLVSQCKFYLENMEQMIKD*KQRKLKKSNVFSLKAYKGLAEVAVKSLCELLVS

Parental  LPHFNFHNNIIVLIVPLMNDVSKSISEMCCEAVKKLFKQDKLGQASLGVIKVISGFVKGRNYEVRPEMLK
          LPHFNFHNNIIVLIVPLMNDVSKSIS.MCCEAVKK.FKQDKLGQAS.GVIKVISGFVKGRNYEVR.EMLK
Retrocopy LPHFNFHNNIIVLIVPLMNDVSKSISGMCCEAVKKWFKQDKLGQASHGVIKVISGFVKGRNYEVRSEMLK

Parental  TFLCLRIKELEVKKDTEDINKP-KKFMTFK-EKRKTLSRMQRKWKKAEEKLERELLEAEASESTERKLKL
          T.LCLR..E.EVKKDTEDINKP.KK...F...KR..LSRMQ.KW.KAEEKLERELLEAEASE.TERKLKL
Retrocopy TLLCLRNQEVEVKKDTEDINKP<KKVHDFQ<RKREKLSRMQKKWNKAEEKLERELLEAEASENTERKLKL

Parental  HTETLNIVFVTYFRILKKAQRS-PLLPAVLEGLAKFAHLINVEFFDDLLVVLHTLIESGDLSYRE
          H.ETLNIVFVTYFRILKKAQ...PLLPAVLEGLAK.A.LI.VEFFDDLLVVLHTLIESGDLSY.E
Retrocopy HMETLNIVFVTYFRILKKAQSV>PLLPAVLEGLAKLAYLIKVEFFDDLLVVLHTLIESGDLSYGE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	12.56 RPM
SRP017611_brain	0.00 RPM	9.37 RPM
SRP017611_kidney	0.00 RPM	11.23 RPM
SRP017611_liver	0.00 RPM	7.83 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1008 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1008 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008033	1 retrocopy	retro_cfam_1008 ,
Rattus norvegicus	ENSRNOG00000013965	1 retrocopy	retro_rnor_1309,