RetrogeneDB ID: retro_cfam_1178

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 25:12084697..12085457(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR2
• Ensembl ID: ENSCAFG00000000244
• Aliases: None
• Description: mitochondrial fission regulator 2 [Source:HGNC Symbol;Acc:21115]

Sequence

>retro_cfam_1178
AGAAATAATATATGGAAACATGAAGAAGAGAAAACGGAATTTTTCCATTCTTTGCAACCAGTCTGGAATTCACTGTCACC
TGCTCTAAGAAAGAATAAATGAATGAAAAATGGTGGGCCTGTAGGAGAAGCTGCCTTTAAAAAGATAGCCGCCCTGGAAG
AGGAGCTCACTTTACTCTGCACCCAGATTGCTGCAATCGTGGGGAGGCAGGGACCCAAAACCAGTGTACATGAGAGCTTC
TTTGACTTGAATGACGAGCCTAGCAGTTTGGGACAACAGTCATCACCAGAGACTGCTGAACTGGGTGCCCAGCTGGATCC
ATTTTCAAGTTCAATGCTTTCCCCTCCTCCTCTGCCTCCTCCTCCACTGCCCCCTCAGCTTTTTTCTCCACAGCCTCTGT
GTTCTTCTCTCACACAGCCAGGATTGAAAAATACACGTGACTCAGATAATTCGGCCAATGAAATGAAAAAACAGCACCCA
GGTGACAACAGTAAGACCAATTACAGTCGTTTAAAAAACCAGGATAAAAAAAGATGTTCCAAACATATTGGATGTTCTAA
AGGACATGAATAAGAATAAGGTTAAGCTTCACGGTATTGAATGGTCACCTGGAGGTAGACCCATTCATAAGAGGAAAAGA
CAAGATTTACATTGGGATCCAGTGTCTTTAATATCCCATGCACGTAAGAAGAAGTTTGCTTTCCAAGAAGATGATTCTTT
TGAGAAAGAAAATAAGTCTTGGGAATCTTCTCCATTTTCC

Alignment

ORF - retro_cfam_1178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.18 %
• Parental protein coverage: 65.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RNNIWKHEEEQKTEFFHSLQPVWNPLSPALRQSKRMKNDGSVGEAAFKKIAALEEELTFLRTQIAAIVGR
          RNNIWKHEEE.KTEFFHSLQPVWN.LSPALR..K.MKN.G.VGEAAFKKIAALEEELT.L.TQIAAIVGR
Retrocopy RNNIWKHEEE-KTEFFHSLQPVWNSLSPALRKNK*MKNGGPVGEAAFKKIAALEEELTLLCTQIAAIVGR

Parental  RGPKTSVHESFFDLNDEPSSLGQQPSPGTAELGAQPDPFSSSMLFPPPPPPPPLPPQLFSPQPLC-SLTQ
          .GPKTSVHESFFDLNDEPSSLGQQ.SP.TAELGAQ.DPFSSSML.............LFSPQPLC.SLTQ
Retrocopy QGPKTSVHESFFDLNDEPSSLGQQSSPETAELGAQLDPFSSSMLXXXXXXXXXXXXXLFSPQPLCSSLTQ

Parental  SGLKNTCDLDNAANEMKKQHPGDNSKTNYSRSKNQE-NQDVPNMLDVLKDL--NKVKLRAIERSPGGKPI
          .GLKNT.D.DN.ANEMKKQHPGDNSKTNYSR.KNQ....DVPN.LDVLKD...NKVKL..IE.SPGG.PI
Retrocopy PGLKNTRDSDNSANEMKKQHPGDNSKTNYSRLKNQD>KKDVPNILDVLKDMNKNKVKLHGIEWSPGGRPI

Parental  HKRKRQDSHWDPVSLISHALKEKFAFQEDDSFEKENRSWESSPFS
          HKRKRQD.HWDPVSLISHA.K.KFAFQEDDSFEKEN.SWESSPFS
Retrocopy HKRKRQDLHWDPVSLISHARKKKFAFQEDDSFEKENKSWESSPFS

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	2.06 RPM
SRP017611_brain	0.00 RPM	0.48 RPM
SRP017611_kidney	0.00 RPM	0.33 RPM
SRP017611_liver	0.00 RPM	0.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1178 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000244	1 retrocopy	retro_cfam_1178 ,
Myotis lucifugus	ENSMLUG00000002331	1 retrocopy	retro_mluc_2227,
Monodelphis domestica	ENSMODG00000017453	1 retrocopy	retro_mdom_1813,
Nomascus leucogenys	ENSNLEG00000014793	1 retrocopy	retro_nleu_1513,
Pan troglodytes	ENSPTRG00000018634	1 retrocopy	retro_ptro_1491,