RetrogeneDB ID: retro_cfam_552

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:44909793..44910542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSCAFG00000007504
• Aliases: None
• Description: adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]

Sequence

>retro_cfam_552
ACTGTCACCGAAAGCAAGTTTGACAACCTGTATGGCTGCCAGGAATCTTTTATAGATGCATCAAGCAGACTATGGATGTG
ATGATTGCAGGCAAGGTGACAGTGGTAGCAGACTAGGGTGATGTGGGCAAAGGTTGTGCCCAGGCCCTGCAGGGTTTTGA
GGCCCGCGTCATCATCACAGAGATCGACCCCATCAATGCACTGTAGGCTGCCATGGAGGGCTATGAGGTGACCACTATGG
ATGAGGCCTGTCAGGATGGCAATACATTTGTCACCACCACAGTTTGTGTTGACATCATCCTTGGCTGGCATTTTGAACAA
ATGAAAGATGATGCCATTGTGTGTAACATTGGACACTTTGACGTGGAGATTGGCATCAAATGGCTGCACGAAAATGCTGT
AGAGAAGGTGAACATCAAGCCCCAGGTGGACCGCTACCGGCTGAAAAATGGGCGCCTTATCCTCCTTTTGGCTGAGGGCC
GGCTGGTCAACCTGGGCTGCGCCATGGGCCATCCCAGCTTTGCGATGAGCAACTCATTCACCAATCAAGTGCTGGCACAG
ATTGAATTGTGGACCCACCCAGACAAGTTCTCTGTTGGGGTTCACTTCCTGCCCAAGAAGCTGGATGAAGCAGTGGCTGA
AGCTCACCTGGGTAAGCTGAATGTGAAGCTGACCAGGCTGACTGAGAAGCAGGCCCAGTACCTGGGCTTGTCCCGTGATG
GCCCCTTCAAGCCCGATCGTTACCTCTAC

Alignment

ORF - retro_cfam_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.45 %
• Parental protein coverage: 57.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVTKSKFDNLYGCRESLIDG-IKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQ
          .VT.SKFDNLYGC.ES.ID..IK...DVMIAGKV.VVA..GDVGKGCAQAL.GF.ARVIITEIDPINAL.
Retrocopy TVTESKFDNLYGCQESFIDA<IKQTMDVMIAGKVTVVAD*GDVGKGCAQALQGFEARVIITEIDPINAL*

Parental  AAMEGYEVTTMDEACQEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNI
          AAMEGYEVTTMDEACQ.GN.FVTTT.CVDIILG.HFEQMKDDAIVCNIGHFDVEI..KWL.ENAVEKVNI
Retrocopy AAMEGYEVTTMDEACQDGNTFVTTTVCVDIILGWHFEQMKDDAIVCNIGHFDVEIGIKWLHENAVEKVNI

Parental  KPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWTHPDKYSVGVHFLPKKLD
          KPQVDRYRLKNGR.I.LLAEGRLVNLGCAMGHPSF.MSNSFTNQVLAQIELWTHPDK.SVGVHFLPKKLD
Retrocopy KPQVDRYRLKNGRLILLLAEGRLVNLGCAMGHPSFAMSNSFTNQVLAQIELWTHPDKFSVGVHFLPKKLD

Parental  EAVAEAHLGKLNVKLTKLTEKQAQYLGLSRDGPFKPDHYRY
          EAVAEAHLGKLNVKLT.LTEKQAQYLGLSRDGPFKPD.Y.Y
Retrocopy EAVAEAHLGKLNVKLTRLTEKQAQYLGLSRDGPFKPDRYLY

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	0.04 RPM	24.57 RPM
SRP017611_brain	0.00 RPM	11.11 RPM
SRP017611_kidney	0.13 RPM	512.78 RPM
SRP017611_liver	0.00 RPM	299.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_552 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_552 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552 ,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,