RetrogeneDB ID: retro_pabe_171

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:22517034..22517937(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005655
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMB5
• Ensembl ID: ENSPPYG00000005654
• Aliases: None
• Description: Proteasome subunit beta type-5 [Source:UniProtKB/Swiss-Prot;Acc:Q5R8S2]

Sequence

>retro_pabe_171
ATGGCTCTGCAGGATGTGTGCAAGTGGCAGTCCCCTGACACCCAGGGACCATCACCTCACCTGCCTCGGGCTGGCGGCTG
GGCTGTGCCCCGGGGCTGTGACCCTCAAACCTTCCTGCAGATCCATGGCCCCAGACTGGCCCATGGCACTACAACCCTGG
CCTTCCGCTTCCGTCATGGAGTCATTGCTGCAGCTGACACGCGTTCCTCCTGTGGCAGCTATGTGGCATGTCCAGCCTCA
TGCAAGGTCATCCCTGTGCACCAGCACCTCCTGGGTACCACCTCTGGCACCTCCGCCGACTGTGCTACCTGGTATCGGGT
ATTACAGCGGGAGCTGCGGCTTCGGGAACTGAGGGACGGTCAGCTGCCCAGTGTGGCCAGTGCTGCCAAGCTCTTGTCAG
CCATGATGTCTCGATACCGGGGACTGGATCTCTGTGTGGCCACTGCCCTGTGCGGCTGGGACCGCTCTGGCCCTGAGCTC
TTCTACGTCTATAGCGACGGCACCCGCCTGCAGGGGGACATCTTCTCTGTGGGCTCTGGATCTCCCTATGCCTACGGTGT
GCTAGACCATGGCTATCGCTACGACATGAGCACCCAGGAAGCCTACGCCCTGGCTCGCTGCGCCGTGGCCCACGCCACCT
ACCGTGATGCCTATTCAGGGGGCTCTGTAGACCTTTTCCACGTGCGGGAGAGTGGATGGGAGCATGTGTCACGCAGTGAT
GCCTGTGTGCTGTACATGGAGTTACAGGAGCTCCTGGAGCCAGAGCCAGAGGAGGATGCCAGCCATGCCCATCCTGAGCC
TGCCACTGCCCACAGAGCTGCAGAAGATACAGAGCTCTCTGTGGGGCCAGGGGAGATGATACCAGGAGACTCCAGGATGC
CAGCAGGGACTGAGACGGTGTGA

Alignment

ORF - retro_pabe_171 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.19 %
• Parental protein coverage: 77.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIEMLHGTTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLARQC
          G....HGTTTLAF.FRHGVI.AAD.R...G.Y.A.....KVI.....LLGT..G..ADC..W.R.L.R..
Retrocopy GPRLAHGTTTLAFRFRHGVIAAADTRSSCGSYVACPASCKVIPVHQHLLGTTSGTSADCATWYRVLQREL

Parental  RIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSV
          R..ELR.....SVA.A.KLL..M...Y.G..L...T..CGWD..GP.L.YV.S.G.R..G..FSVGSGS.
Retrocopy RLRELRDGQLPSVASAAKLLSAMMSRYRGLDLCVATALCGWDRSGPELFYVYSDGTRLQGDIFSVGSGSP

Parental  YAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLH
          YAYGV.D.GY.YD.....AY.LAR.A...ATYRDAYSGG.V.L.HVRE.GW..VS......L.
Retrocopy YAYGVLDHGYRYDMSTQEAYALARCAVAHATYRDAYSGGSVDLFHVRESGWEHVSRSDACVLY

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	0.06 RPM	43.51 RPM
SRP007412_cerebellum	0.00 RPM	27.36 RPM
SRP007412_heart	0.06 RPM	24.84 RPM
SRP007412_kidney	0.00 RPM	43.79 RPM
SRP007412_liver	0.03 RPM	28.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_171 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_171 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_95
Pan troglodytes	retro_ptro_97
Gorilla gorilla	retro_ggor_156
Callithrix jacchus	retro_cjac_35
Oryctolagus cuniculus	retro_ocun_176
Bos taurus	retro_btau_11
Sus scrofa	retro_sscr_90
Canis familiaris	retro_cfam_75
Equus caballus	retro_ecab_18

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634, retro_hsap_95,
Gorilla gorilla	ENSGGOG00000026856	2 retrocopies	retro_ggor_1232, retro_ggor_156,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171 ,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,