RetrogeneDB ID: retro_ptro_416

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:33399298..33399749(+)
• Located in intron of: ENSPTRG00000002413

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK3
• Ensembl ID: ENSPTRG00000020742
• Aliases: None
• Description: adenylate kinase 3 [Source:HGNC Symbol;Acc:17376]

Sequence

>retro_ptro_416
GGAGACCTGCTCCAGGATCAACATGCTGCGGGGCACAGAAATTAATGTGTTAGCTAACGCTTTCATTGACCAAAGGAAAC
TCATCCGAGATGATGTCATGACTCAGCTGGCCCTATATGAGCTGAAAAATCTCACTTAGTATAGCTAGCTGTTGGGTGGT
TTTCCATGGACACTTCCACAGGCAGAAGCCCTAGACTAAGCTTCTTAGACAGACAAAGTGATTAGCCCGAATGTGCCCTT
TGAGGTCATTAAACAATGCCTTACTGCTCGCTAGATTCATCCTGCCAGTGGCTGAGTCTACAACATTGAATTCAACCCTC
CCAAAACTGTGGGCACTGATGATCTGACTGGGGATCCTCTCATTCAGCATGAGGATGATAAACCAGAGACGGTTATCAAA
AGACTAAAGGCTTATGAAGCCCAAACAAAGCCAGTCCTGGAACATTACCAA

Alignment

ORF - retro_ptro_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 79.37 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDLLGG-TMLRGTEIGVLAKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALHRAYQ
          GDLL....MLRGTEI.VLA.AFIDQ.KLI.DDVMT.LAL.ELKNLT.YS.LL.GFP.TLPQAEAL..A..
Retrocopy GDLLQD>NMLRGTEINVLANAFIDQRKLIRDDVMTQLALYELKNLT*YS*LLGGFPWTLPQAEALD*AS*

Parental  IDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDLTGEPLIQREDDKPETVIKRLKAYE
          .D.VI..NVPFEVIKQ.LTAR.IHPASG.VYNIEFNPPKTVG.DDLTG.PLIQ.EDDKPETVIKRLKAYE
Retrocopy TDKVISPNVPFEVIKQCLTAR*IHPASG*VYNIEFNPPKTVGTDDLTGDPLIQHEDDKPETVIKRLKAYE

Parental  DQTKPVLEYYQ
          .QTKPVLE.YQ
Retrocopy AQTKPVLEHYQ

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	0.09 RPM	12.53 RPM
SRP007412_cerebellum	0.07 RPM	11.87 RPM
SRP007412_heart	0.06 RPM	56.95 RPM
SRP007412_kidney	0.08 RPM	76.21 RPM
SRP007412_liver	0.16 RPM	33.68 RPM
SRP007412_testis	0.00 RPM	4.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_416 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_416 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_416 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_555
Gorilla gorilla	retro_ggor_503

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002640	3 retrocopies	retro_amel_1009, retro_amel_1916, retro_amel_1931,
Bos taurus	ENSBTAG00000017147	1 retrocopy	retro_btau_323,
Callithrix jacchus	ENSCJAG00000011188	1 retrocopy	retro_cjac_1940,
Equus caballus	ENSECAG00000011235	2 retrocopies	retro_ecab_317, retro_ecab_914,
Echinops telfairi	ENSETEG00000000829	1 retrocopy	retro_etel_57,
Felis catus	ENSFCAG00000028063	2 retrocopies	retro_fcat_162, retro_fcat_1982,
Homo sapiens	ENSG00000147853	3 retrocopies	retro_hsap_1163, retro_hsap_3228, retro_hsap_555,
Gorilla gorilla	ENSGGOG00000028122	3 retrocopies	retro_ggor_2195, retro_ggor_503, retro_ggor_908,
Loxodonta africana	ENSLAFG00000001126	1 retrocopy	retro_lafr_205,
Microcebus murinus	ENSMICG00000013112	3 retrocopies	retro_mmur_1474, retro_mmur_1559, retro_mmur_1579,
Myotis lucifugus	ENSMLUG00000017272	1 retrocopy	retro_mluc_535,
Macaca mulatta	ENSMMUG00000000143	2 retrocopies	retro_mmul_2032, retro_mmul_898,
Mustela putorius furo	ENSMPUG00000005006	2 retrocopies	retro_mputfur_1163, retro_mputfur_890,
Nomascus leucogenys	ENSNLEG00000008885	3 retrocopies	retro_nleu_2638, retro_nleu_2653, retro_nleu_948,
Oryctolagus cuniculus	ENSOCUG00000011411	1 retrocopy	retro_ocun_716,
Otolemur garnettii	ENSOGAG00000007477	2 retrocopies	retro_ogar_3482, retro_ogar_3492,
Pongo abelii	ENSPPYG00000019245	3 retrocopies	retro_pabe_2676, retro_pabe_3588, retro_pabe_967,
Pan troglodytes	ENSPTRG00000000827	4 retrocopies	retro_ptro_2024, retro_ptro_2154, retro_ptro_2449, retro_ptro_2870,
Pan troglodytes	ENSPTRG00000020742	5 retrocopies	retro_ptro_1785, retro_ptro_2180, retro_ptro_2895, retro_ptro_416 , retro_ptro_796,
Pteropus vampyrus	ENSPVAG00000015751	1 retrocopy	retro_pvam_269,
Sus scrofa	ENSSSCG00000023595	1 retrocopy	retro_sscr_641,
Ictidomys tridecemlineatus	ENSSTOG00000000021	1 retrocopy	retro_itri_933,
Tupaia belangeri	ENSTBEG00000008054	3 retrocopies	retro_tbel_1463, retro_tbel_3247, retro_tbel_3397,
Tursiops truncatus	ENSTTRG00000016524	1 retrocopy	retro_ttru_1036,
Vicugna pacos	ENSVPAG00000009187	1 retrocopy	retro_vpac_137,