RetrogeneDB ID: retro_cfam_376

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:31077542..31078013(-)
• Located in intron of: ENSCAFG00000001788

Retrocopy information

• Ensembl ID: ENSCAFG00000001789
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSCAFG00000015398
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_cfam_376
ATGGCGACCTACGGGCAGAGCTGTGCGCAGCCAATGTGTGTTCCTCCATCCTATGTTGACCTTGGCAAGGCTGCCAGAGA
TATTTTCAACAAAGGATTTGGTTTTGGGTTGGTGAAACTGGATGTGAAAACAAAGTCATGCAGTGGTGTGGAACTCTCAA
CATCTGGTTCATCTAATACAGACACTGGTAAAGTTACTGGAACCTTGGAGACCAGATATAAATGGTGTGAGTATGGCCTG
ACTTTCACAGAAAAGTGGAACACCGATAACACTCTGGGAACAGAAATCGCAATTGAAGACCAGATCTGTCAAGGTTTGAA
ACTGACATTTGATACCATCTTTTCACCAAACACAGGAAAGAAAAATAGTAAAATCAAGCCTTCTTACAAGCGGGAGTGTA
TAAACCTTGGTTGTGACGTTGACTTTGATTTTGCTGGACCTGCAATCCATGGTTCAGCCGTCTTTGGTTAT

Alignment

ORF - retro_cfam_376 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.9 %
• Parental protein coverage: 53.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATYGQSCARPMCVPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE
          MATYGQSCA.PMCVPPSY.DLGKAARDIFNKGFGFGLVKLDVKTKSCSGVE.STSGSSNTDTGKVTGTLE
Retrocopy MATYGQSCAQPMCVPPSYVDLGKAARDIFNKGFGFGLVKLDVKTKSCSGVELSTSGSSNTDTGKVTGTLE

Parental  TKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDV
          T.YKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDT.FSPNTGKK..KIK.SYKRECINLGCDV
Retrocopy TRYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTIFSPNTGKKNSKIKPSYKRECINLGCDV

Parental  DFDFAGPAIHGSAVFGY
          DFDFAGPAIHGSAVFGY
Retrocopy DFDFAGPAIHGSAVFGY

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	0.08 RPM	141.62 RPM
SRP017611_brain	0.00 RPM	143.07 RPM
SRP017611_kidney	0.00 RPM	294.86 RPM
SRP017611_liver	0.00 RPM	56.92 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_376 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_376 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000000985	1 retrocopy	retro_cfam_1728,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376 ,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,