RetrogeneDB ID: retro_cfam_1345

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:55277137..55277635(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSCAFG00000028510
• Aliases: None
• Description: family with sequence similarity 206, member A [Source:HGNC Symbol;Acc:1364]

Sequence

>retro_cfam_1345
CTCGTGGATCGTTACTTCACTGGCTGGTACAAAGCCGATGTCAAAGGCAAACCCTGTGAGGACCACTGTATACTACAGCG
CTCCAACTGAATATGTGTCATCACATTGGCAGACTCTCATCCAGTTTTCAAAGTGGAAAAACAATTAAAAGCATCTCCTA
TCAAATCAGTACTAACTGTAGCCGACTTCAGAACAAGGTCTCTGGGAAATTTAAGCGAGGGGCAGTTTCTAATAGAGCTT
GCACCTCTGTGTACGATTTACTGCTCAGATGGAGAAGAATATACCATATCTCGCTGTGTTAGAGGACGGCTGATGGAAAT
GAATGAAAACATTCTCCATAAGCCATCTATTCTTCAAGAGAAGCCGTCAACCGAAGGCTACATTGCAGTTGTATTGCCCA
AATTTGAAGAAAGTAAAAGCATAACGGAAGGGTTACTGACACAGAAACAGTATGAAGCAGTCGTGGGGAAGCGCATTAAT
GCCCCAACAGCTCCATCA

Alignment

ORF - retro_cfam_1345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 92.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVDRYFTRWYKADVKGKPCEDHCILQHSNRICVITLAESHPVL-QSGKTIKSISYQISTNCSRLQNKVS-
          LVDRYFT.WYKADVKGKPCEDHCILQ.SN.ICVITLA.SHPV..QSGKTIKSISYQISTNCSRLQNKVS.
Retrocopy LVDRYFTGWYKADVKGKPCEDHCILQRSN*ICVITLADSHPVF<QSGKTIKSISYQISTNCSRLQNKVS>

Parental  GKFKRGAQFLTELAPLCKIYCSDGEEYTISSCVRGRLMEVNENILHKPSILQEKPSTEGYIAVVLPKFEE
          G....G.QFL.ELAPLC.IYCSDGEEYTIS.CVRGRLME.NENILHKPSILQEKPSTEGYIAVVLPKFEE
Retrocopy GNLSEG-QFLIELAPLCTIYCSDGEEYTISRCVRGRLMEMNENILHKPSILQEKPSTEGYIAVVLPKFEE

Parental  SKSITEGLLTQKQYEEVVVKRINATTAPS
          SKSITEGLLTQKQYE.VV.KRINA.TAPS
Retrocopy SKSITEGLLTQKQYEAVVGKRINAPTAPS

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	15.16 RPM
SRP017611_brain	0.00 RPM	12.62 RPM
SRP017611_kidney	0.00 RPM	24.76 RPM
SRP017611_liver	0.00 RPM	2.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1345 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1345 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345 ,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583,