RetrogeneDB ID: retro_cfam_743

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 16:53999679..54000416(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000008535
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMA6
• Ensembl ID: ENSCAFG00000013409
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 6 [Source:HGNC Symbol;Acc:9535]

Sequence

>retro_cfam_743
ATGTCCCGTGGTTCCAGCGCTGGGTTTGACCGTCACATTACCATTTTTTCACCTGAGGGCCGGCTCTACCGAGTAGAATA
TGCTTTTAAGGCTATTAACCAGGGTGGCCTTACATCGGTAGCTGTCAGAGGGAAAGACTGTGCAGTAATTGTCACACAGA
AGAAAGTACCTGACAAATTATTGGATTCCAGCACAGTGACTCACTTATTCAAGATAACTGAAAACATTGGCTGTGTGATG
ACAGGAATGACAGCTGACAGCAGATCCCAGGTACAGAGAGCACGCTATGAGGCAGCTAATTGGAAATACAAGTATGGGTA
TGAGATTCCTGTGGACAGGCTGGCAAAAGAATTGCTGATATTTCTCAGGTCTACACACAGAATGCTGAAATGAGGCCTCT
CGGTTGTTGTATGATTTTAATTGGTATAGATGAAGAACAAGGCCCTCAGGTGTACAAGTGTGATCCTGCAGGTTACTACT
GTGGGTTTAAAGCCACTGCAGCAGGAGTTAAACAAACGGAGTCAACCAGCTTCCTTGAAAAAAAAGTGAAGAATAAATTT
GATTGGACATTTGAACAGACAGTGGAAACTGCAATTACATGCCTATCAACTGTTCTATCAATTGATTTCAAACCTTCAGA
AATAGAAGTTGGAGTAGTTACAGTTGAAAATCCTAAATTCAGGATTCTTTCAGAAGCAGAGATTGACGCTCACCTTGTTG
CCCTAGCAGAGAGAGAC

Alignment

ORF - retro_cfam_743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
          MSRGSSAGFDRHITIFSPEGRLY.VEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
Retrocopy MSRGSSAGFDRHITIFSPEGRLYRVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF

Parental  KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLC-KRIADISQVYTQNAEMRPLGCCMI
          KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVD.L..KRIADISQVYTQNAEMRPLGCCMI
Retrocopy KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDRLA<KRIADISQVYTQNAEMRPLGCCMI

Parental  LIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSID
          LIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFL...VK.KFDWTFEQTVETAITCLSTVLSID
Retrocopy LIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLXXXVKNKFDWTFEQTVETAITCLSTVLSID

Parental  FKPSEIEVGVVTVENPKFRILSEAEIDAHLVALAERD
          FKPSEIEVGVVTVENPKFRILSEAEIDAHLVALAERD
Retrocopy FKPSEIEVGVVTVENPKFRILSEAEIDAHLVALAERD

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	32.93 RPM
SRP017611_brain	0.00 RPM	22.87 RPM
SRP017611_kidney	0.13 RPM	62.27 RPM
SRP017611_liver	0.07 RPM	12.04 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_743 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_743 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013409	2 retrocopies	retro_cfam_1581, retro_cfam_743 ,
Echinops telfairi	ENSETEG00000004892	1 retrocopy	retro_etel_1775,
Felis catus	ENSFCAG00000026276	1 retrocopy	retro_fcat_973,
Homo sapiens	ENSG00000100902	2 retrocopies	retro_hsap_1228, retro_hsap_4923,
Macropus eugenii	ENSMEUG00000016537	1 retrocopy	retro_meug_1217,
Microcebus murinus	ENSMICG00000000083	4 retrocopies	retro_mmur_104, retro_mmur_165, retro_mmur_752, retro_mmur_80,
Myotis lucifugus	ENSMLUG00000010228	1 retrocopy	retro_mluc_822,
Macaca mulatta	ENSMMUG00000016544	1 retrocopy	retro_mmul_343,
Mustela putorius furo	ENSMPUG00000016288	1 retrocopy	retro_mputfur_1089,
Mus musculus	ENSMUSG00000021024	1 retrocopy	retro_mmus_654,
Otolemur garnettii	ENSOGAG00000008492	10 retrocopies	retro_ogar_1273, retro_ogar_1397, retro_ogar_1928, retro_ogar_1950, retro_ogar_2021, retro_ogar_2073, retro_ogar_2274, retro_ogar_2488, retro_ogar_2521, retro_ogar_3089,
Pan troglodytes	ENSPTRG00000006264	2 retrocopies	retro_ptro_3297, retro_ptro_844,
Rattus norvegicus	ENSRNOG00000007114	4 retrocopies	retro_rnor_1724, retro_rnor_1960, retro_rnor_854, retro_rnor_924,
Tupaia belangeri	ENSTBEG00000011241	17 retrocopies	retro_tbel_1304, retro_tbel_1415, retro_tbel_1789, retro_tbel_2028, retro_tbel_2466, retro_tbel_2519, retro_tbel_3227, retro_tbel_3280, retro_tbel_3535, retro_tbel_4181, retro_tbel_4183, retro_tbel_4357, retro_tbel_4465, retro_tbel_4495, retro_tbel_509, retro_tbel_602, retro_tbel_725,