RetrogeneDB ID: retro_cfam_312

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:58000711..58001292(-)
• 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_312
GGCTGCTCTCCCAAGATGGTGGCTGCACTGGGTGGAGTACTGAAGCACTGGGAGCCAGGCATCCTGAGGGAGGTGACAGG
AGCCTCAGCTGCTTGGTGAATGGTAACCTTCCACTACTAGTCTGAAATGCTAGCTTTAAAACGTTTCTCTTCCAGTGGAA
AGCCCAACCATGCAGACATCTTCTTGCTCATAAATTTACAGTATGTTTTAGAAGTGGAGATAATTAATAATGGAACAAGA
AACCTAACTGCACTCAATGTTAATAAGCTTGCCAGCAAGCACAGACAGGAAAAGAAAAGAAGCTGAGCTAGGCCCAGTGC
TGGTGTCTCCCTAAAGAGCCTGCAGCTCTTCCAGACCATACACAAGAACTTTAGAGACTGTAAATGACAAGAAAAAATCA
TAGTCATGGAAGATGTTGTTTATACACCCCTCACATCAGGTGGAAAACTATAAAAGCAAGCAAAGGGAGGAGTGCACTGA
GCCATGTACACAAAATAGTTTAAAAATACTTTAGAGATGTGTAAAGCCGAAAGATACTGTAGCGTTCATAAGCCCTGCAA
CCACAGAAGGAGGTTGCCCTT

Alignment

ORF - retro_cfam_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.24 %
• Parental protein coverage: 92.96 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GCSPKMAAPPG-EYFSVGSQVSCRTCQEQRLQGE-VVAFDYQSKMLALKCPSSSGKPNHADI-LLINLQY
          GCSPKM.A..G.EY.S.GSQ.S....QE..L.GE..V.F.Y.S.MLALK..SSSGKPNHADI.LLINLQY
Retrocopy GCSPKMVAALG>EY*STGSQAS*GR*QEPQLLGE<MVTFHY*SEMLALKRFSSSGKPNHADIFLLINLQY

Parental  VSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEK
          V.EVEIIN..T.....L..LNV.KLASK.R.EK..........SAGVSL...QLFQTIHK...DCK.QEK
Retrocopy VLEVEIINNGTRN---LTALNVNKLASKHRQEKKRS*ARP---SAGVSLKSLQLFQTIHKNFRDCK*QEK

Parental  NIVVMEEVVITP-PYQVEN-CKGKEG-SALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAAL
          .I.VME.VV.TP...QVEN..K...G.SALSHV.KIV.K.FRDV.S.KIL.RS.A.QPQKE.AL
Retrocopy -IIVMEDVVYTP>SHQVEN>IKASKGRSALSHVHKIV*KYFRDV*SRKIL*RS*ALQPQKEVAL

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_312 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_312 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,