RetrogeneDB ID: retro_cfam_1486

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:1697739..1698737(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000008682
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cfam_1486
CCAGTGTACGCCTGGAAGGGTGAAACGGATGAGGAGTACCTGTGGTGCATTTAGCAGACACTACTTCAAGGACAGGACCC
TCAACACGATTCTGGATGACGGAGGTGACCTTTACCAATCTCATCCACACCAAGTACCCACAGTTCCTATCAGGCATCCA
AGGCATTTCTGAAGAGACCACAACAGGGGTTCATAATCTATACAAGATGATGGCCAATGGGGAGCTGAAGGTGCCTGCCA
TCAATGTGAACGACTCTGTCACCAAAAGCAAGTTTGACAACCTGTATGGCTGCCGGGAGTCTCTTATAGATGGCATCAAG
TGGGCTACGGATGTGATGATTGCAGGCAAGGTGGCAGTGGTAGCAGGCTATGGCGATGTGGACAAAGGTTGTGCCCAGGC
CCTGCGGGGTTTTGGGGCCCACATCATCATCACGGAGATCGACCCCATCAATGCACTGCAGGCTGCCATGGAGGGCTATG
AGGTGACCACTATGGATGAGGCCTGTCAGGATGGCAATATATTTGTCACCACCACAGGCTATGTTGACATCATCCTTGGC
CAGCACTTTGAACAGATGAAAAATGATGCCATCGTGTGTAACATCAGACACTTTGACGTGGAGATTGAGGTCAAATGGCT
GAGCGAAAATGCCATAGAGAAAGTGAATATCAAGCCCCAGGTGGACCGCTACCAGCTGAAAAATGGGTGCCGTATCATCC
TGTTGGCTGAGGGCCGGCTGGTCAACCTGGGCTGTGCCATGGGCCATCCCAGCTTTGTGATGAGCCACTCATTCACCAAT
CAAGTGCTGGCACAGATAGAATTGTGGACCCACCCAGACAAGTACTCTGTTGGGGTTCACTTCCTGCCCAAAAAGGTGGA
TGAAGCAGTGGCTGAAGCTCACCTGGGTAAGCTGAATGTGAAGCTGACCAAGCTGACTGAGGAGCAAGCCCAGTACCTGG
GCTTGTCCCGTGATGGCCCCTTCAAGCCCGATCATTAC

Alignment

ORF - retro_cfam_1486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.37 %
• Parental protein coverage: 76.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PVYAWKGETDEEYLWCIEQTLY-FKDGP-LNMILDDGGDL-TNLIHTKYPQLLSGIRGISEETTTGVHNL
          PVYAWKGETDEEYLWCI.QTL.....GP.LN.ILDDGGDL.TNLIHTKYPQ.LSGI.GISEETTTGVHNL
Retrocopy PVYAWKGETDEEYLWCI*QTLL<SRTGP<LNTILDDGGDL>TNLIHTKYPQFLSGIQGISEETTTGVHNL

Parental  YKMMANGKLKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRG
          YKMMANG.LKVPAINVNDSVTKSKFDNLYGCRESLIDGIK.ATDVMIAGKVAVVAGYGDV.KGCAQALRG
Retrocopy YKMMANGELKVPAINVNDSVTKSKFDNLYGCRESLIDGIKWATDVMIAGKVAVVAGYGDVDKGCAQALRG

Parental  FGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDV
          FGA..IITEIDPINALQAAMEGYEVTTMDEACQ.GNIFVTTTG.VDIILG.HFEQMK.DAIVCNI.HFDV
Retrocopy FGAHIIITEIDPINALQAAMEGYEVTTMDEACQDGNIFVTTTGYVDIILGQHFEQMKNDAIVCNIRHFDV

Parental  EIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVLAQIELWT
          EI.VKWL.ENA.EKVNIKPQVDRY.LKNG.RIILLAEGRLVNLGCAMGHPSFVMS.SFTNQVLAQIELWT
Retrocopy EIEVKWLSENAIEKVNIKPQVDRYQLKNGCRIILLAEGRLVNLGCAMGHPSFVMSHSFTNQVLAQIELWT

Parental  HPDKYSVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGLSRDGPFKPDHY
          HPDKYSVGVHFLPKK.DEAVAEAHLGKLNVKLTKLTE.QAQYLGLSRDGPFKPDHY
Retrocopy HPDKYSVGVHFLPKKVDEAVAEAHLGKLNVKLTKLTEEQAQYLGLSRDGPFKPDHY

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	0.17 RPM	24.57 RPM
SRP017611_brain	0.40 RPM	11.11 RPM
SRP017611_kidney	13.01 RPM	512.78 RPM
SRP017611_liver	7.61 RPM	299.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1486 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1486 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,