RetrogeneDB ID: retro_cfam_1843

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:20692217..20692539(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSCAFG00000014379
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_cfam_1843
GCCAGCTGTGGCTGCTCTCCCAAGACAAGCAGCTCCTCCGGGCAAGTAGTTCTGTGTTGGGAGCCACGTGTTGTGCTGGA
CGTGCCAGGAGAAGCGGCTGCAGGATGAGGTGGTAGCCTTTGACTACCAGTCCAAAATGCTGGCTTTAAAATGTTCCTCT
TTCAGTGGAAAGCCGAACCATGCAGACATCTTGCTCATAAACTTACAGTATGTTTCAGAAGTGGAAATAATTAATGACTG
AACAGAAACCCCTTCTCCCCTAGCTTCATTCAGTGTTAGTAAGGTTGTAAAACATTTTAGAGATGTGGAAAGCCAAAAGA
TA

Alignment

ORF - retro_cfam_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 50.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGRGCSPK-MAAPPGEYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQ
          A..GCSPK..AAPPG..F.VGS.V.C.TCQE.RLQ.EVVAFDYQSKMLALKC.S.SGKPNHADILLINLQ
Retrocopy ASCGCSPK>QAAPPGK*FCVGSHVLCWTCQEKRLQDEVVAFDYQSKMLALKCSSFSGKPNHADILLINLQ

Parental  YVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKL
          YVSEVEIIND.TETP.PLAS..VSK.....R.....K.
Retrocopy YVSEVEIIND*TETPSPLASFSVSKVVKHFRDVESQKI

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	19.40 RPM
SRP017611_brain	0.00 RPM	12.07 RPM
SRP017611_kidney	0.00 RPM	12.08 RPM
SRP017611_liver	0.00 RPM	5.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1843 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843 , retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,