RetrogeneDB ID: retro_cfam_428

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:51700127..51700394(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLIPR2
• Ensembl ID: ENSCAFG00000030686
• Aliases: None
• Description: GLI pathogenesis-related 2 [Source:HGNC Symbol;Acc:18007]

Sequence

>retro_cfam_428
GAGAACTTGGCATGGGCTTCCTATGATCAGACAGAAAAGGAGATGGCTGATAGATGGTACAGTGAAATCAAGCACTACAA
CTTTCACCAGCCTGACTTCATCTCCAGGACTGGGTACTTCACAGATGATATCAAAGAATACAAAGAAGATGGGAGTAGGG
AAGGCACTTGCAAGTGAGGGGTCTTCCTTCATGGTGGCCTGATACTTCCTAGCAGGGAATGTTGTCAACTAGGCCTCTTT
GAAGAAAATATCTTGCCTCCAAAGAAG

Alignment

ORF - retro_cfam_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.74 %
• Parental protein coverage: 58.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ENLAWASYDQTGKEVADRWYSEIKNYNFQQPGFTSGTGHFTAMVWKNTKKMG-VGKASASDGSSFVVARY
          ENLAWASYDQT.KE.ADRWYSEIK.YNF.QP.F.S.TG.FT....K..K..G.VGKA.AS.GSSF.VA.Y
Retrocopy ENLAWASYDQTEKEMADRWYSEIKHYNFHQPDFISRTGYFTDDI-KEYKEDG>VGKALASEGSSFMVA*Y

Parental  FPAGNVVN-QGFFEENVLPPKK
          F.AGNVVN..G.FEEN.LPPKK
Retrocopy FLAGNVVN<LGLFEENILPPKK

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	6.93 RPM
SRP017611_brain	0.08 RPM	7.15 RPM
SRP017611_kidney	0.00 RPM	5.35 RPM
SRP017611_liver	0.00 RPM	3.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_428 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030686	1 retrocopy	retro_cfam_428 ,
Dasypus novemcinctus	ENSDNOG00000008950	1 retrocopy	retro_dnov_2040,
Dipodomys ordii	ENSDORG00000012831	1 retrocopy	retro_dord_342,
Felis catus	ENSFCAG00000012762	2 retrocopies	retro_fcat_115, retro_fcat_1587,
Microcebus murinus	ENSMICG00000017673	1 retrocopy	retro_mmur_1525,
Myotis lucifugus	ENSMLUG00000011791	2 retrocopies	retro_mluc_1145, retro_mluc_475,
Mus musculus	ENSMUSG00000028480	1 retrocopy	retro_mmus_2458,
Rattus norvegicus	ENSRNOG00000014838	1 retrocopy	retro_rnor_2217,
Tupaia belangeri	ENSTBEG00000009276	2 retrocopies	retro_tbel_1646, retro_tbel_4682,