RetrogeneDB ID: retro_ptro_3297

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: Y:20811696..20812434(+)
• Located in intron of: ENSPTRG00000022489

Retrocopy information

• Ensembl ID: ENSPTRG00000040695
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMA6
• Ensembl ID: ENSPTRG00000006264
• Aliases: None
• Description: Pan troglodytes proteasome (prosome, macropain) subunit, alpha type, 6 (PSMA6), mRNA. [Source:RefSeq mRNA;Acc:NM_001246657]

Sequence

>retro_ptro_3297
ATGTCCCATGGTTCCAGCGCTGGTTTTGACCGCCACATTACCATTTTTTCACCCGAGGGTCGGCTCTACCAAGTAGAATA
TGCTTTTAAGGCTATTAACCAGGGTGGCCTTACATCAGTAGCTGTCAGAGGTTAAGACTGTGTAGTAATTGTCCCACAGA
AGAAAGTACCTGACAAATTATTGGATTCCAGCATAGTGACTCACTTATTCAAGATAACTGAAAACATTGGTTGTGTTACG
ACCGGAATGACAGCTGACAGCAGATCCCAGGTACAGAGGGCACGCTATGAGGCAGCTAACTGGAAATACAAGTATGGCTA
TGAAATTCCTGTGGACATGCTGTGTAAAAGAATTGCCGATATTTCTCAGGTCTACACACGCAATGCTGAAATGAGGCCTC
TTGGTTGTTGTATGATTTTAATTGGTATAGATGAAGAGCAAGGCCCTCAGGTATATAAGTGTGATCCTGCAGGTTACTAT
TGTGGGTTTAAAGCCACTGCAGTGGGAGTTAAACAAACTGAGACAACCAGCTTCCTTGAAAAAAAAGTGAAGAAGAAATT
TGACTGGACATTTGAACAGACTTTGGAAACTGCAATTACATGCCTGTCTACTGTTCTATCAGTTGATTTCAAACCTTCAG
AAATAGAAGTTGGAGTAGTGACAGTTGAAAATCCTGAATTCAGGATTCTTACAGAAGCAGACATTGATGCTCACCTTGTT
GCTCTAGCAGAGAGAGAC

Alignment

ORF - retro_ptro_3297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKLLDSSTVTHLF
          MS.GSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRG.DC.VIV.QKKVPDKLLDSS.VTHLF
Retrocopy MSHGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRG*DCVVIVPQKKVPDKLLDSSIVTHLF

Parental  KITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCCMIL
          KITENIGCV.TGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYT.NAEMRPLGCCMIL
Retrocopy KITENIGCVTTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTRNAEMRPLGCCMIL

Parental  IGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLEKKVKKKFDWTFEQTVETAITCLSTVLSIDF
          IGIDEEQGPQVYKCDPAGYYCGFKATA.GVKQTE.TSFL...VKKKFDWTFEQT.ETAITCLSTVLS.DF
Retrocopy IGIDEEQGPQVYKCDPAGYYCGFKATAVGVKQTETTSFLXXXVKKKFDWTFEQTLETAITCLSTVLSVDF

Parental  KPSEIEVGVVTVENPKFRILTEAEIDAHLVALAERD
          KPSEIEVGVVTVENP.FRILTEA.IDAHLVALAERD
Retrocopy KPSEIEVGVVTVENPEFRILTEADIDAHLVALAERD

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
SRP007412_brain_prefrontal_cortex	0.16 RPM	37.36 RPM
SRP007412_cerebellum	0.14 RPM	34.20 RPM
SRP007412_heart	0.32 RPM	50.92 RPM
SRP007412_kidney	0.18 RPM	52.36 RPM
SRP007412_liver	0.46 RPM	95.62 RPM
SRP007412_testis	0.32 RPM	167.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3297 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3297 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4923

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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,