RetrogeneDB ID: retro_cfam_2119

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:100568125..100568591(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPV17
• Ensembl ID: ENSCAFG00000032367
• Aliases: None
• Description: MpV17 mitochondrial inner membrane protein [Source:HGNC Symbol;Acc:7224]

Sequence

>retro_cfam_2119
CTAACAGTTGGGTTCCTTATGGGCCTGGGTGACATTATCTCATGGCAGCTGGTAGAGAGGTTAGGTCTGTAGGAACATCA
GACTGGCTGGACCCTGACCATGGTCTCTCTGGGCTGCGGCTTGTGGGCCCTGTAGTCAGAGGCTGGTACGGGGTTTTGAA
CCAGTTCATCCACAGCACCACCAAGGTAGATGCAGTAAAGAAGATGCTATTGGATCTGGGGGGCTTTGCCCCATGTTTTC
TAGGCCGTTTCCTTCGACTGGTAAGAGCACTCAATGGACTCTCAGCCCAGGACAACTGGGCCAAGTTACAGCAAGACTAT
TGTGATGCCCTCATCACCAACTATTATCTGGCCTGCCATGAATTTAAGCCAACTTCTAGCTGGTTCCCCTTCATTACGTA
TTAGCTATTGTCCAGTGTGTTGCTCTTATCTGGAACTCCTACCTCTTCTGGAAGGTACACCAGCTC

Alignment

ORF - retro_cfam_2119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.7 %
• Parental protein coverage: 88.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTAGSLMGLGDIISQQLVEKRGLRGHQTGRTLTMAFLGCGF-VGPVVGGWYRVLDRLIPGTAKADALKKM
          LT.G.LMGLGDIIS.QLVE..GL..HQTG.TLTM..LGCG..VGPVV.GWY.VL...I..T.K.DA.KKM
Retrocopy LTVGFLMGLGDIISWQLVERLGL*EHQTGWTLTMVSLGCGL<VGPVVRGWYGVLNQFIHSTTKVDAVKKM

Parental  LLDQGGFAPCFLGCFLPLVGALNGLSAQDNWAKLRRDYPDALLTNYY-LWPAVQL-ANFYLVPLHYRLAV
          LLD.GGFAPCFLG.FL.LV.ALNGLSAQDNWAKL..DY.DA.L...Y..WPA..L.ANF.LVPLHY.LA.
Retrocopy LLDLGGFAPCFLGRFLRLVRALNGLSAQDNWAKLQQDYCDA-LITNY>IWPAMNL>ANF*LVPLHYVLAI

Parental  VQCVAVIWNSYLSWKAHRL
          VQCVA.IWNSYL.WK.H.L
Retrocopy VQCVALIWNSYLFWKVHQL

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	12.43 RPM
SRP017611_brain	0.00 RPM	6.83 RPM
SRP017611_kidney	0.07 RPM	9.18 RPM
SRP017611_liver	0.00 RPM	1.81 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2119 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032367	1 retrocopy	retro_cfam_2119 ,
Felis catus	ENSFCAG00000015150	1 retrocopy	retro_fcat_1943,