RetrogeneDB ID: retro_cfam_26

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:36185450..36186104(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSCAFG00000002708
• Aliases: None
• Description: None

Sequence

>retro_cfam_26
AGCGGGCTGCCGAGCGCGGTGCGCCACCCGACCAACGAGTGCGCCCCCTACCAGCGCCGCGCCTCGGGCCTGCCCATCGC
GCCGTGCGGCGCCATCGCCAACAGCCTCTTCAACGACTCCTTCTCGCTGTGGCACCGGCGCCGCGCCGGCGGGCCGTACG
TCGAGGTGCCGCTCGACCGCACCGGCATCGCCTGGTGGACCGACTGCCACGTCAAGTTCCGCAACCCGCCGCTGGTGAAC
GGCAGCCTGGCGCTGGCCTTCCACGGCACCGCGCCGCCGCCCAACTGGCCCCGGCCCGTGTACGCGCTGAGCCCGGACCC
GAACAACACCGGCTTCGTCAACCAGGACTTCGTGGTGTGGATGCGCACGGCGGCGCTGCCCACGTTCCGCAAGCTGTACG
CGCGCATCCGCCAGGGCAACTACTCCGCGGGGCTGCCGCGCGGCTCCTACGTGGTCAACATCACCTACAACTACCCGGTG
CGCGCCTTCGGCGGCCGCAAGCTCGTGGTCCTCAGCAACATCTCGTGGATGGGGGGCAAGAACCCGTTCCTGGGCATCGC
CTACCTGGCCGTCGGCTCCCTCTGCATCCTCGTGGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGAACG
ACGAGGACGAGGAT

Alignment

ORF - retro_cfam_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.35 %
• Parental protein coverage: 58.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGDSGALLNPSKECEPY-RRNEDKPIAPCGAIANSMFNDTLELFLVGNESYP-TPIPLKKKGIAWWTDKN
          .G...A...P..EC.PY.RR....PIAPCGAIANS.FND...L........P....PL...GIAWWTD..
Retrocopy SGLPSAVRHPTNECAPYQRRASGLPIAPCGAIANSLFNDSFSLWHRRRAGGPYVEVPLDRTGIAWWTDCH

Parental  VKFRNPP-GDQSLEERFKGTTNPVNWVKPVYMLDSEPDNNGFINEDFIVWMRTAALPTFRKLYRLIERKS
          VKFRNPP....SL...F.GT..P.NW..PVY.L...P.N.GF.N.DF.VWMRTAALPTFRKLY..I.R..
Retrocopy VKFRNPPLVNGSLALAFHGTAPPPNWPRPVYALSPDPNNTGFVNQDFVVWMRTAALPTFRKLYARI-RQG

Parental  DLHPTLPAGRYYLNITYNYPVHSFDGRKRMILSTISWMGGKNPFLGIAYIAIGSISFLLGVVLLVINHKY
          .....LP.G.Y..NITYNYPV..F.GRK...LS.ISWMGGKNPFLGIAY.A.GS...L.G.V.LV....Y
Retrocopy NYSAGLPRGSYVVNITYNYPVRAFGGRKLVVLSNISWMGGKNPFLGIAYLAVGSLCILVGFVMLVVYIRY

Parental  RNSSN
          .....
Retrocopy QDQND

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	0.42 RPM	129.69 RPM
SRP017611_brain	1.27 RPM	240.24 RPM
SRP017611_kidney	4.56 RPM	112.92 RPM
SRP017611_liver	13.63 RPM	47.50 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_26 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_26 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_26 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26 ,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,