RetrogeneDB ID: retro_cfam_1979

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:27138074..27139423(+)
• Located in intron of: None

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_1979
CGTGAGTGTATCTTGATCCACGTTGGCCAGGCAGGTGTCTAGACCAGCAATACCTGCTGGGAGCTCTATTGCCTGGAACA
CGGCGTTCAGCCCGATGACCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTG
AGACGGGCACTGGCAAGCACGTGCCCAGGGCAGTGTTTATAGACCTGGAGCCCACAGTCACTGATGAAGTTCGCACTGGC
ACCTACTGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGAGGGCACTA
CGCCATTGGCAAGGAGATCACTGACCTTGTCTTAGACCGAATTTGGAAACTGGCTGACCAGTGCACGGGTCTTCAGAGCT
TCTTGGTTTTCCACAGCTTTGGAGGGGGAGCCGGTTCTGGGTTCACCTCCCTGCTGATGGAACGTCTCTCTGTCGATTAT
GGCAAGAAGTCCAAGCTAAAGTTCTCCATATACCCTGCCCTCCAGGTGTCCACAGCTGTAGTAGACCCTACAACTCCATC
CTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAACGAGGCCATCTATGACATCTGTTGTAG
AAACCTCGATATTGAGTGCCCAACCTACACTAATCTAAGCAGGTTGATAGGTCAGATTGTGTCCTCCATCACTGCTTCCC
TCAGATTTGATGGAGCCGTGAATGTGGATCTGACGGAGTTCCAGACCAACCTGGTGCCCTATCCCTGCATCCACTTCCCT
CTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCATG
CTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGTAAATACATGGCTTGCTGCCTGTTGTACCGTGGCG
ACGTGGTTCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAGACCAAGCATACCATCCAGTTTGTGGACTGGTGCCCC
ACTGGCTTCAAAGTAGGCATTAACTACCAGCCTCCCACTGTGGTACCCGGTGGAGACCTGGCCAAAGTACAGTGAGCTGT
GTGTATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCTCCTGGACCACAAGTTTGACCTGATGTATGCCAAGC
GTGCCTTTGTTCACTGGTATGTGGGTGAGGGCATGAAGGAAGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTGCCCTG
TAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTTAAAGGAGAGGGTGAAGAAGAAAGAGAGGAATAC

Alignment

ORF - retro_cfam_1979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.46 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
          RECI.IHVGQAGV...N.CWELYCLEHG.QPD.QMPSDKTIGGGDDSFNTFFSETG.GKHVPRAVF.DLE
Retrocopy RECILIHVGQAGV*TSNTCWELYCLEHGVQPDDQMPSDKTIGGGDDSFNTFFSETGTGKHVPRAVFIDLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
          PTV.DEVRTGTY.QLFHPEQLITGKEDAANNYARGHY.IGKEI.DLVLDRI.KLADQCTGLQ.FLVFHSF
Retrocopy PTVTDEVRTGTYCQLFHPEQLITGKEDAANNYARGHYAIGKEITDLVLDRIWKLADQCTGLQSFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEP-YNSILTTHTTLEHSDCAFMVDNEAIY
          GGG.GSGFTSLLMERLSVDYGKKSKL.FSIYPA.QVSTAVV.P.YNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy GGGAGSGFTSLLMERLSVDYGKKSKLKFSIYPALQVSTAVVDP<YNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DIC.RNLDIE.PTYTNL.RLI.QIVSSITASLRFDGA.NVDLTEFQTNLVPYP.IHFPLATYAPVISAEK
Retrocopy DICCRNLDIECPTYTNLSRLIGQIVSSITASLRFDGAVNVDLTEFQTNLVPYPCIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
          AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTK..IQFVDWCPTG
Retrocopy AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKHTIQFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPPTVVPGGDLAKVQ.AVCMLSNTTAIAEAWA.LDHKFDLMYAKRAFVHWYVGEGM.EGEFSE
Retrocopy FKVGINYQPPTVVPGGDLAKVQ*AVCMLSNTTAIAEAWALLDHKFDLMYAKRAFVHWYVGEGMKEGEFSE

Parental  AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          AREDMAAL.KDYEEVGVDSV.GEGEEE.EEY
Retrocopy AREDMAAL*KDYEEVGVDSVKGEGEEEREEY

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	1.18 RPM	465.89 RPM
SRP017611_brain	2.94 RPM	647.84 RPM
SRP017611_kidney	0.20 RPM	186.36 RPM
SRP017611_liver	0.22 RPM	50.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1979 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1979 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,