RetrogeneDB ID: retro_cfam_2000

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:27693798..27694751(-)
• Located in intron of: ENSCAFG00000030895

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000008640
• Aliases: None
• Description: None

Sequence

>retro_cfam_2000
AAGCGTGAATGCATCTCCATCTATGTTGACCAGGCACGTGTCCAGATCAGCAATGCCTGCTGGGAGCTCTATTGCCTGGA
ACACAGCATTCAGCCTGATGGCCAGATGCCAAGTGACGAGACCATTGGAGGAGGCGATGACTCCTTCAACACCTTCTTCA
GTGAGATGGGCACTGGCAAGCATGTGCCAGGGCAGTGTTTGTAGACCTGGAGCCCATAATCGTTAATGAAGTTCGCACTG
GCACCTACTGCCAGCTCTTCCATCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGAGGGCAC
TACACTATTGGCAAAGAGATCATTGACCTTGTCTTGGACTGAATTCGGAAATTGGATGACCAGTGCATGGGTCTTCAGGG
CTTCTTAGTTTTCCACAGCTTTGGAGGGGGAACCAGTTCTGGGTTCACCTCCCTGCTGATGGAACGTCTCTGTCGATTAT
GGCAAGAAGTCCAAGCTAGAGTTCTCCATCTACCTTGCCCTCCAGGTGTCCACAGCTATAGTAGACCCTACAACTCCATC
CTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAACGAGGCTATCTATGACATCTGTTGTAG
AAACCTCGATATTGAATGCCCAACCTACACTAATCTAAACAAGTTGATAGGTCAGATTGTGTCCTCCATCACTGCTTCCC
TCAGATTTGACAGAGCCCTGAATGTGGATCTGATGGAGTTCCAGACTAACCTGGTGCCCTATCCCCACATCCACTTCCCT
CTGGCCACATGTACCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCATG
CTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCACCATGGTAAATACATGGCTTGCTGCCTGTTGTAT

Alignment

ORF - retro_cfam_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 70.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVP-RAVFVD
          .RECISI.V.QA.VQI.NACWELYCLEH.IQPDGQMPSD.TIGGGDDSFNTFFSE.G.GKHVP.RAVFVD
Retrocopy KRECISIYVDQARVQISNACWELYCLEHSIQPDGQMPSDETIGGGDDSFNTFFSEMGTGKHVP<RAVFVD

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          LEP....EVRTGTY.QLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD.IRKL.DQC.GLQGFLVFH
Retrocopy LEPIIVNEVRTGTYCQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD*IRKLDDQCMGLQGFLVFH

Parental  SFGGGTGSGFTSLLMER-LSVDYGKKSKLEFSIYPAPQVSTAVVEP-YNSILTTHTTLEHSDCAFMVDNE
          SF.GG..S.....L.....SVDYGKKSKLEFSIY.A.QVSTA.V.P.YNSILTTHTTLEHSDCAFMVDNE
Retrocopy SF-GGGTSSGFTSLLME>VSVDYGKKSKLEFSIYLALQVSTAIVDP<YNSILTTHTTLEHSDCAFMVDNE

Parental  AIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIS
          AIYDIC.RNLDIE.PTYTNLN.LI.QIVSSITASLRFD.ALNVDL.EFQTNLVPYP.IHFPLAT..PVIS
Retrocopy AIYDICCRNLDIECPTYTNLNKLIGQIVSSITASLRFDRALNVDLMEFQTNLVPYPHIHFPLATCTPVIS

Parental  AEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLY
          AEKAYHEQLSVAEITNACFEPANQMVKCDP.HGKYMACCLLY
Retrocopy AEKAYHEQLSVAEITNACFEPANQMVKCDPHHGKYMACCLLY

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	0.08 RPM	465.89 RPM
SRP017611_brain	0.48 RPM	647.84 RPM
SRP017611_kidney	0.00 RPM	186.36 RPM
SRP017611_liver	0.00 RPM	50.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2000 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2000 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Canis familiaris	ENSCAFG00000005248	1 retrocopy	retro_cfam_1124,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000 , retro_cfam_463, retro_cfam_926,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Canis familiaris	ENSCAFG00000010412	1 retrocopy	retro_cfam_1418,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,