RetrogeneDB ID: retro_cfam_1875

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:35561561..35562229(-)
• Located in intron of: ENSCAFG00000015817

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL9
• Ensembl ID: ENSCAFG00000017710
• Aliases: None
• Description: methyltransferase like 9 [Source:HGNC Symbol;Acc:24586]

Sequence

>retro_cfam_1875
CTATTTATCCAAATATATCACCTTTTTGTGTCATCTGTTTTTAACCTGTTTATGTCTAGAACATCTTCATTGGGTTTCTA
GGAAGAGGCTCAATGTTTGTGTTTTCACCAGACCAGTTTCAGGGACTGCTAAAAATTAATCCAGACTGGAAAACCCATAG
ACTTCTTGATTTCAGTGCTGGAAATGGAGAAGTCACAAAAATTATGAGCCCTCACTTTGAAGAGATGTATGCCACTGAGC
TATCTGAAATTATGATATGGCAGCTTCAGAAGAAGAAATACAGAGTACTTGGTATAAATGAATAACAGAATAAAGGCTTC
CAGTACAATGTCATCAGTTGCTTCAATTTGCTAGACTGCTATGATGAGCCCATAAGCTATTAAAAGATATCAGAAGTGTC
TTGGAGCCGACCAGAGGCAGGGCCATTCTTGCCCTGTTTTTACCCTTTCTTCACTATGCAGAAAACAGGTGGCAAGTGGG
AAAAACCATCAGAAATTTTAGAAATCAAGGTACAGAATTGAGAAGAACAAGTGAGTAGTCTGCCTAAAGTTTTCAGAAAA
GCTGGTTTTGTAACTGAAGATTTCACCAGACCACCATACCTGTGTGAAAGCAACACGTATAATGACTACTACATTCTGGA
TGATGCAGTTTTTGTTTTCAAACCAGTA

Alignment

ORF - retro_cfam_1875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFIQLYHSFVSSVFSLFMSRTS-INGLLGRGSMFVFSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIM
          LFIQ.YH.FVSSVF.LFMSRTS...G.LGRGSMFVFSPDQFQ.LLKINPDWKTHRLLD..AG.GEVTKIM
Retrocopy LFIQIYHLFVSSVFNLFMSRTS<FIGFLGRGSMFVFSPDQFQGLLKINPDWKTHRLLDFSAGNGEVTKIM

Parental  SPHFEEIYATELSETMIWQLQKKKYRVLGINEWQKTGFQYDVISCLNLLDRCDQPLT-LLKDIRSVLEPT
          SPHFEE.YATELSE.MIWQLQKKKYRVLGINE.Q..GFQY.VISC.NLLD..D.P...LLKDIRSVLEPT
Retrocopy SPHFEEMYATELSEIMIWQLQKKKYRVLGINE*QNKGFQYNVISCFNLLDCYDEPIS<LLKDIRSVLEPT

Parental  RGRVILALVL-PFHPYVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGFVIEAFTRLPYLCEGDM
          RGR.ILAL.L.PF.......GGKWEKPSEILEIK.QN.EEQV.SLP.VFRKAGFV.E.FTR.PYLCE...
Retrocopy RGRAILALFL>PFFT-MQKTGGKWEKPSEILEIKVQN*EEQVSSLPKVFRKAGFVTEDFTRPPYLCESNT

Parental  YNDYYVLDDAVFVLKPV
          YNDYY.LDDAVFV.KPV
Retrocopy YNDYYILDDAVFVFKPV

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	87.74 RPM
SRP017611_brain	0.00 RPM	48.51 RPM
SRP017611_kidney	0.00 RPM	74.16 RPM
SRP017611_liver	0.00 RPM	8.56 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1875 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1875 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003533	2 retrocopies	retro_amel_402, retro_amel_704,
Canis familiaris	ENSCAFG00000017710	1 retrocopy	retro_cfam_1875 ,
Callithrix jacchus	ENSCJAG00000020564	1 retrocopy	retro_cjac_4083,
Mustela putorius furo	ENSMPUG00000016801	2 retrocopies	retro_mputfur_1323, retro_mputfur_1610,
Rattus norvegicus	ENSRNOG00000025940	1 retrocopy	retro_rnor_2623,
Sus scrofa	ENSSSCG00000030373	1 retrocopy	retro_sscr_441,
Tupaia belangeri	ENSTBEG00000003816	2 retrocopies	retro_tbel_1726, retro_tbel_2084,
Tursiops truncatus	ENSTTRG00000015624	4 retrocopies	retro_ttru_1100, retro_ttru_1466, retro_ttru_163, retro_ttru_467,