RetrogeneDB ID: retro_cfam_1868

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:3483472..3484216(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000012775
• Aliases: None
• Description: None

Sequence

>retro_cfam_1868
ATGTGCCATACCATCACCCTTACCAGGGAGGACCTGGAGAAGCTCAAAGCCTAGAGAGTGAACCTGCAGATCTGCAGCGG
CTATGACCATGTTGACCTCAAGGCTGTTGGCCAGCTCAGGATCACCACGTGCACTACTGCACTCGGGGCGATGGAAGAGA
ATGCTGACTCCAGCATCTCCCACATCCTTCACCTGTACCTCCAGAACACGTGGTTGTACCAGGTGCTGCAGGAAGGCACA
CTGGTCCAGGGTGTTGAGGAGATCCAGGTGGACACCTCACAAGCAGCCTGCGTCCACGGGGAGATGCTGGGCCTTATCGG
CCTTTGTTGCACAGGGCAGGTGGCTGCTGTTCCAGTCAAGGACTTTGGATCCAGCAGCATATTTTAGGAGCCCTACTTCC
AGGATGGAACGGAGCAGTCCCTGGGTGTGCAGAAGGTCTGCGCCCTGCAGGATTGGCTGTGTGAGAGCGACTGCGTCTCC
TTGTCCTGTAATCTCAGTGAACATCACCACCACCTCACCAAGGACTTTACTGGAAAGCACAGGAGGCATGAAGCATTCCT
TGCGAATGCTGTCCACAGTGGGCGGGTGAATGAGCAAGCCTTGGCCTAAGCCCTCAAGGAAGGCAGGACACAAGGGGCAG
CCCTCAAAGGGCATGAATCCGAGCCTTTCAGCTTTGCTCGGTGTCCCTTGAAAGATGCACTGAATCTCACTTGTAAGCCC
CACATAGCTTGGTGTAGTGAGCAG

Alignment

ORF - retro_cfam_1868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.71 %
• Parental protein coverage: 55.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYHTITLTREDLEKFKALRVIVRIGSGYDNVDIKAAGELGIAVCNIPSAAVEETADSTICHILNLYRRNT
          M.HTITLTREDLEK.KA.RV...I.SGYD.VD.KA.G.L.I..C.....A.EE.ADS.I.HIL.LY..NT
Retrocopy MCHTITLTREDLEKLKA*RVNLQICSGYDHVDLKAVGQLRITTCTTALGAMEENADSSISHILHLYLQNT

Parental  WLYQALREGTRVQSVEQIREVASGAARIRGETLGLIGFGRTGQAVAVRAKAFGFSVIFYDPYLQDGIERS
          WLYQ.L.EGT.VQ.VE.I....S.AA...GE.LGLIG...TGQ..AV..K.FG.S.IF..PY.QDG.E.S
Retrocopy WLYQVLQEGTLVQGVEEIQVDTSQAACVHGEMLGLIGLCCTGQVAAVPVKDFGSSSIF*EPYFQDGTEQS

Parental  LGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQMRQGAFLVNAARGGLVDEKALAQALKEGRI
          LGVQ.V..LQD.L..SDCVSL.CNL.EH.HHL..DFT.K..R..AFL.NA...G.V.E.ALA.ALKEGR.
Retrocopy LGVQKVCALQDWLCESDCVSLSCNLSEHHHHLTKDFTGKHRRHEAFLANAVHSGRVNEQALA*ALKEGRT

Parental  RGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQ
          .GAAL..HESEPFSFA..PLKDA.NL.C.PH.AW.SEQ
Retrocopy QGAALKGHESEPFSFARCPLKDALNLTCKPHIAWCSEQ

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	0.00 RPM	51.41 RPM
SRP017611_brain	0.00 RPM	9.45 RPM
SRP017611_kidney	0.00 RPM	17.57 RPM
SRP017611_liver	0.00 RPM	2.90 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1868 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1868 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012775	1 retrocopy	retro_cfam_1868 ,
Callithrix jacchus	ENSCJAG00000012539	2 retrocopies	retro_cjac_1866, retro_cjac_2528,
Homo sapiens	ENSG00000175029	1 retrocopy	retro_hsap_403,
Otolemur garnettii	ENSOGAG00000024152	2 retrocopies	retro_ogar_1393, retro_ogar_45,
Pongo abelii	ENSPPYG00000002746	10 retrocopies	retro_pabe_1706, retro_pabe_1710, retro_pabe_1711, retro_pabe_1719, retro_pabe_1737, retro_pabe_1750, retro_pabe_1773, retro_pabe_3228, retro_pabe_3230, retro_pabe_3587,