RetrogeneDB ID: retro_ptro_3137

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:80463581..80464359(+)
• Located in intron of: ENSPTRG00000022060

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA1
• Ensembl ID: ENSPTRG00000003385
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]

Sequence

>retro_ptro_3137
TTTAGAAACCAGTATGACAATGATATCATTGTCTGGAGCAGGATTCATCAAACTGAATATGCAATGGAAGCTGTTAAACA
AGGTTCAGCCACAGTTGGTCTGAAATAAAAAACCCATGCAGTATTGGTTGCATTGAAAAGGGCACCATCGGAGCTTGCAG
CTCATCAGAAAAAAATTCTCCATATTGACAATCATATTGGTATCTCAATTGCAGGGCTTACTGATGACGGTAAACTGTTA
TGTAATTTTATGTGCCAGGAGTGTTTCGATTCCAGATTTGTATCTGATAGACCACTTCCTGTGTCTTCTCTTGTATCTCT
AATTGGAAGCAAGACCCAAATATCAACACAACAATATGGCTGGAGACCATATGGTGTTAGGCTACTTACTGCTGGTTATA
ATGATATGGGCCTCACATTTTCCAAACCTGGTCATCTGCTGACTATTTTGACTACAGAGCTACGTCCACTGGGGCCCGTT
CTCAGTCAGCTCGTACTTACTTGGAGAGACATATGTCTAAATTTATGGAATACAATTTAAATGAACTGGTTAAACATGGT
CTGCATGCCTTAAGAGAGACAATTCCTGCAGAACAGGACATAACTACAAAAATGTTTCCATTGGAATTGCTGGTAATAAT
TTGGAGTTTACAATCTATCATGATGATGATGATGTGTCTCCAATCCTGGAAGGTCTTGAAGAAAGGCCACAGAGAAAGGC
AAAGCCTGCTCAACCTGCTGATGAACCAGCAGAAAAGGCTGATGAACCAATGGAACAT

Alignment

ORF - retro_ptro_3137 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.53 %
• Parental protein coverage: 97.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKILHVDNHIG
          FRNQYDND..VWS...RIHQ.EYAMEAVKQGSATVGLK.KTHAVLVALKRA.SELAAHQKKILH.DNHIG
Retrocopy FRNQYDNDIIVWS---RIHQTEYAMEAVKQGSATVGLK*KTHAVLVALKRAPSELAAHQKKILHIDNHIG

Parental  ISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM-
          ISIAGLT.D..LLCNFM.QEC.DSRFV.DRPLPVS.LVSLIGSKTQI.TQ.YG.RPYGV.LL.AGY.DM.
Retrocopy ISIAGLTDDGKLLCNFMCQECFDSRFVSDRPLPVSSLVSLIGSKTQISTQQYGWRPYGVRLLTAGYNDM<

Parental  GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTT-KN
          GPHIFQT..SA.YFD.RA.S.GARSQSARTYLERHMS.FME.NLNELVKHGL.ALRET.PAEQD.TT.KN
Retrocopy GPHIFQTWSSADYFDYRATSTGARSQSARTYLERHMSKFMEYNLNELVKHGLHALRETIPAEQDITT<KN

Parental  VSIGIVGKDLEFTIY-DDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH
          VSIGI.G..LEFTIY.DDDDVSP.LEGLEERPQRKA.PAQPADEPAEKADEPMEH
Retrocopy VSIGIAGNNLEFTIYHDDDDVSPILEGLEERPQRKAKPAQPADEPAEKADEPMEH

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	0.04 RPM	40.83 RPM
SRP007412_cerebellum	0.00 RPM	37.53 RPM
SRP007412_heart	0.00 RPM	53.37 RPM
SRP007412_kidney	0.03 RPM	47.15 RPM
SRP007412_liver	0.00 RPM	65.34 RPM
SRP007412_testis	0.00 RPM	44.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3137 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3137 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3137 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4720
Pongo abelii	retro_pabe_3664
Macaca mulatta	retro_mmul_2509

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002440	2 retrocopies	retro_amel_1733, retro_amel_1903,
Bos taurus	ENSBTAG00000006564	1 retrocopy	retro_btau_1833,
Choloepus hoffmanni	ENSCHOG00000005395	11 retrocopies	retro_chof_155, retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus	ENSECAG00000024086	1 retrocopy	retro_ecab_1078,
Felis catus	ENSFCAG00000011381	1 retrocopy	retro_fcat_972,
Homo sapiens	ENSG00000129084	1 retrocopy	retro_hsap_4720,
Gorilla gorilla	ENSGGOG00000001416	1 retrocopy	retro_ggor_2933,
Macropus eugenii	ENSMEUG00000011112	1 retrocopy	retro_meug_71,
Myotis lucifugus	ENSMLUG00000009251	4 retrocopies	retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta	ENSMMUG00000016446	1 retrocopy	retro_mmul_2509,
Mustela putorius furo	ENSMPUG00000013199	4 retrocopies	retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus	ENSMUSG00000030751	1 retrocopy	retro_mmus_831,
Nomascus leucogenys	ENSNLEG00000017705	1 retrocopy	retro_nleu_1990,
Oryctolagus cuniculus	ENSOCUG00000000439	2 retrocopies	retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii	ENSOGAG00000011622	3 retrocopies	retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps	ENSOPRG00000013677	1 retrocopy	retro_opri_370,
Pongo abelii	ENSPPYG00000003466	2 retrocopies	retro_pabe_1883, retro_pabe_3664,
Pan troglodytes	ENSPTRG00000003385	1 retrocopy	retro_ptro_3137 ,
Sarcophilus harrisii	ENSSHAG00000015626	1 retrocopy	retro_shar_217,
Ictidomys tridecemlineatus	ENSSTOG00000006270	2 retrocopies	retro_itri_1470, retro_itri_987,
Tupaia belangeri	ENSTBEG00000012037	3 retrocopies	retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta	ENSTSYG00000003869	2 retrocopies	retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos	ENSVPAG00000008820	3 retrocopies	retro_vpac_344, retro_vpac_648, retro_vpac_82,