RetrogeneDB ID: retro_ptro_409

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:14075872..14076220(+)
• Located in intron of: ENSPTRG00000002308

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUTF2
• Ensembl ID: ENSPTRG00000008248
• Aliases: None
• Description: None

Sequence

>retro_ptro_409
GGAGGCAAGCCCATGTGGGAGATGACTGGACCCATCTTCATTCAACGTTCAGTTATTGAGTTCTATAACAATAGAACTCA
ACTCAGCACAATTTACATTGACATATCACGCCTTAGGCGGGAAGGAGAGCAGCTCGAGGGGAAGGCTGCCATTGTAAAGA
AGCCATCCAGCCTTCTGTTCCACAAAATCCAGCGTAGCATCATGGTGCAGGACCGTCAGCCCACACCCGCTAACTGCATC
CTCAGCATGGTTGTGGGCCAGCCAAATGCCAATGAAGACCCCATTATGGGGCTCCACCAGATGTTCCTATGAAAGGACAT
AATGGATGCTTGGGTTCGCCCTCATGAC

Alignment

ORF - retro_ptro_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.93 %
• Parental protein coverage: 91.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDKPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQ
          G.KP.WE..G..FIQ.....F.N.RTQL..IYID.S.L..EG.Q..GKAAIV.K.SSL.F.KIQ.SI..Q
Retrocopy GGKPMWEMTGPIFIQRSVIEFYNNRTQLSTIYIDISRLRREGEQLEGKAAIVKKPSSLLFHKIQRSIMVQ

Parental  DHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTND
          D.QPTP..CI.SMVVGQ..A.EDPIMG.HQMFL.K.I.DAWV...D
Retrocopy DRQPTPANCILSMVVGQPNANEDPIMGLHQMFL*KDIMDAWVRPHD

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	65.22 RPM
SRP007412_cerebellum	0.00 RPM	27.07 RPM
SRP007412_heart	0.00 RPM	18.04 RPM
SRP007412_kidney	0.00 RPM	30.55 RPM
SRP007412_liver	0.03 RPM	19.21 RPM
SRP007412_testis	0.00 RPM	19.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_409 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_409 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_409 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_544

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 103 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017548	5 retrocopies	retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Choloepus hoffmanni	ENSCHOG00000003059	3 retrocopies	retro_chof_1386, retro_chof_1619, retro_chof_2488,
Callithrix jacchus	ENSCJAG00000016015	14 retrocopies	retro_cjac_1328, retro_cjac_2247, retro_cjac_2562, retro_cjac_2864, retro_cjac_2913, retro_cjac_2953, retro_cjac_2978, retro_cjac_3126, retro_cjac_3299, retro_cjac_4044, retro_cjac_4173, retro_cjac_587, retro_cjac_777, retro_cjac_924,
Equus caballus	ENSECAG00000021530	1 retrocopy	retro_ecab_151,
Felis catus	ENSFCAG00000008167	3 retrocopies	retro_fcat_154, retro_fcat_743, retro_fcat_845,
Homo sapiens	ENSG00000102898	7 retrocopies	retro_hsap_1322, retro_hsap_1480, retro_hsap_1858, retro_hsap_207, retro_hsap_4181, retro_hsap_4854, retro_hsap_544,
Gorilla gorilla	ENSGGOG00000023925	5 retrocopies	retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Loxodonta africana	ENSLAFG00000031037	1 retrocopy	retro_lafr_623,
Macropus eugenii	ENSMEUG00000009874	11 retrocopies	retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus	ENSMLUG00000025175	3 retrocopies	retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta	ENSMMUG00000012038	6 retrocopies	retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica	ENSMODG00000005517	6 retrocopies	retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mustela putorius furo	ENSMPUG00000006737	4 retrocopies	retro_mputfur_229, retro_mputfur_614, retro_mputfur_714, retro_mputfur_962,
Mus musculus	ENSMUSG00000008450	1 retrocopy	retro_mmus_232,
Nomascus leucogenys	ENSNLEG00000004889	7 retrocopies	retro_nleu_1295, retro_nleu_1791, retro_nleu_1855, retro_nleu_2374, retro_nleu_2384, retro_nleu_2953, retro_nleu_731,
Oryctolagus cuniculus	ENSOCUG00000006322	1 retrocopy	retro_ocun_115,
Ochotona princeps	ENSOPRG00000013727	4 retrocopies	retro_opri_1089, retro_opri_1102, retro_opri_1170, retro_opri_229,
Procavia capensis	ENSPCAG00000015344	1 retrocopy	retro_pcap_56,
Pongo abelii	ENSPPYG00000007472	7 retrocopies	retro_pabe_1101, retro_pabe_1229, retro_pabe_1515, retro_pabe_3421, retro_pabe_3772, retro_pabe_433, retro_pabe_502,
Pan troglodytes	ENSPTRG00000008248	7 retrocopies	retro_ptro_1001, retro_ptro_1239, retro_ptro_2835, retro_ptro_3230, retro_ptro_338, retro_ptro_409 , retro_ptro_903,
Pteropus vampyrus	ENSPVAG00000016605	1 retrocopy	retro_pvam_843,
Sarcophilus harrisii	ENSSHAG00000006100	1 retrocopy	retro_shar_274,
Sus scrofa	ENSSSCG00000030295	3 retrocopies	retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Drosophila melanogaster	FBgn0031145	1 retrocopy	retro_dmel_27,