RetrogeneDB ID: retro_cfam_1551

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 34:7006496..7007180(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GID8
• Ensembl ID: ENSCAFG00000012749
• Aliases: None
• Description: GID complex subunit 8 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:15857]

Sequence

>retro_cfam_1551
ATGAGTTATGCAGAAAGACCCGATGAAATCACGAAAGATGAGTGGATGGAGAAACTCAATAACTTGCATGTCCAGCGGGC
AGACATGAACCGCCTCATCATGAACTACTTGGTCACAGAGGGCTTTAAGGAAGCAGCAGAGAAATCTCGAATGGAATCTG
GGATTGAACCTAGTGTGGACCTAGAAACACTTGATGAGCGGATCAAAATCCGTGAGATGATCCTGAAAGGCCAGATCCAG
GAGGCTATTGCGTTGATCAACAGTCTCCATCCGGAGCTCCTGGCCACAAACCGGTACCTTTACTTCCACCTGCAACAACA
GCACCTCATAGAGCTGATCCGCCAGCGTGAGACCAAGGCGGCGCTGGAGTTCGCACAGACCCAGCTGGCCGAGCAAGGTG
AGGAGAGCAGGGAATGCCTGACGGAGACGGAGAGCACCCTGGCCCTGCTGGCCCTTGACAACCCAGAAGAGTTGCCGTTT
GGGGACCTGCTTCACATGATGCAGAGGTAGAAGGTGTGGAGTGAAGTTAACCAAGCTGTCCTAGATTATGAAAATCATGA
GTCAATACCCAAGCTGGCAAAATTACTGAAACTACTCCTTTGGGCTCAGAATGAGCTGGACCAGAAGAAAGTAAAATATC
CCAAAATGACAGACCTCAGCAAAGGTGTGATCGAGGAGCCCAAG

Alignment

ORF - retro_cfam_1551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYAEKPDEITKDEWMEKLNNLHVQRADMNRLIMNYLVTEGFKEAAEKFRMESGIEPSVDLETLDERIKI
          MSYAE.PDEITKDEWMEKLNNLHVQRADMNRLIMNYLVTEGFKEAAEK.RMESGIEPSVDLETLDERIKI
Retrocopy MSYAERPDEITKDEWMEKLNNLHVQRADMNRLIMNYLVTEGFKEAAEKSRMESGIEPSVDLETLDERIKI

Parental  REMILKGQIQEAIALINSLHPELLDTNRYLYFHLQQQHLIELIRQRETEAALEFAQTQLAEQGEESRECL
          REMILKGQIQEAIALINSLHPELL.TNRYLYFHLQQQHLIELIRQRET.AALEFAQTQLAEQGEESRECL
Retrocopy REMILKGQIQEAIALINSLHPELLATNRYLYFHLQQQHLIELIRQRETKAALEFAQTQLAEQGEESRECL

Parental  TEMERTLALLAFDNPEESPFGDLLHMMQRQKVWSEVNQAVLDYENRESTPKLAKLLKLLLWAQNELDQKK
          TE.E.TLALLA.DNPEE.PFGDLLHMMQR.KVWSEVNQAVLDYEN.ES.PKLAKLLKLLLWAQNELDQKK
Retrocopy TETESTLALLALDNPEELPFGDLLHMMQR*KVWSEVNQAVLDYENHESIPKLAKLLKLLLWAQNELDQKK

Parental  VKYPKMTDLSKGVIEEPK
          VKYPKMTDLSKGVIEEPK
Retrocopy VKYPKMTDLSKGVIEEPK

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	0.29 RPM	29.69 RPM
SRP017611_brain	1.51 RPM	24.61 RPM
SRP017611_kidney	0.46 RPM	19.94 RPM
SRP017611_liver	0.36 RPM	9.06 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1551 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1551 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012749	1 retrocopy	retro_cfam_1551 ,
Myotis lucifugus	ENSMLUG00000016381	2 retrocopies	retro_mluc_417, retro_mluc_418,
Monodelphis domestica	ENSMODG00000016835	1 retrocopy	retro_mdom_1208,
Mus musculus	ENSMUSG00000027573	1 retrocopy	retro_mmus_1267,
Otolemur garnettii	ENSOGAG00000013834	1 retrocopy	retro_ogar_2550,
Rattus norvegicus	ENSRNOG00000010180	1 retrocopy	retro_rnor_2248,
Sorex araneus	ENSSARG00000013102	2 retrocopies	retro_sara_396, retro_sara_598,