RetrogeneDB ID: retro_ptro_3256

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:105118655..105119437(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHB
• Ensembl ID: ENSPTRG00000009376
• Aliases: None
• Description: Pan troglodytes prohibitin (PHB), mRNA. [Source:RefSeq mRNA;Acc:NM_001246403]

Sequence

>retro_ptro_3256
ATGGCTGCCAAAGTGTTTGTGTCCATTGGCAAGTTTGGCCTGGCCTTAGCTGTTGTAGGAAGCATGCTGAACTCTGCCTT
ATATAATGTGGATGCTGGTCACAGAGCTGTCATCTTTGACCGATTCTGTGGAGTACAGGACATTGTGGTAGGGGAAGGGA
CTCACTTTCCTATCCCATGGGTACAGAAACCAATTATCTTTGACTGCCATTCTCGACCACTTAATGTACCAGTCATCACT
GGTAGCAAAGACTTACAGAATGTCAACATCACACTGTACATCCTCTCCTGGCCTGTCGCTAGCCAGCTTCCTTGCATCTT
CACCAGCATCAGAGAGGACTATGATGAGCGTGTGCTGCCATCCATCACTACCAAGATCCTCAAGTCGATGGTGTCTCACT
TTGATGCTGGAGAACTAATCACCCAGAGAGAGCTGCTCTCCAGGCAGGTGAGTGACAATCTTACGGAGTGAGCAGCCACC
TTTGGGCTCATCCTGGACGATGTGTCCTTGACACATCCAACCTTCGGGAAGGAGTTCACAGAAGCAGTGGAAGCCAAAGA
GGTGGATCAGCAGGAAGCAGAGAGGGCCAGATTTGTGGTGGAAAAGGCTGAGCAGCAGAAAATAGCAGCCATAATCTCTG
CTGAGGTTGACTCCATGGCAGCCAAGCTGATCCCCAACTCACTGGCCACTGCAGGGGACGGCCTGATCGAGCTGAGCGTG
CTGGAAGCTGCAGAGGACATCACATACCAGCTCTCAGCTCTGAGAACATCACCTACCTGCCT

Alignment

ORF - retro_ptro_3256 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.64 %
• Parental protein coverage: 95.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAKVFESIGKFGLALAVAGGVVNSALYNVDAGHRAVIFDRFRGVQDIVVGEGTHFLIPWVQKPIIFDCR
          MAAKVF.SIGKFGLALAV.G...NSALYNVDAGHRAVIFDRF.GVQDIVVGEGTHF.IPWVQKPIIFDC.
Retrocopy MAAKVFVSIGKFGLALAVVGSMLNSALYNVDAGHRAVIFDRFCGVQDIVVGEGTHFPIPWVQKPIIFDCH

Parental  SRPRNVPVITGSKDLQNVNITLRILFRPVASQLPRIFTSIGEDYDERVLPSITTEILKSVVARFDAGELI
          SRP.NVPVITGSKDLQNVNITL.IL..PVASQLP.IFTSI.EDYDERVLPSITT.ILKS.V..FDAGELI
Retrocopy SRPLNVPVITGSKDLQNVNITLYILSWPVASQLPCIFTSIREDYDERVLPSITTKILKSMVSHFDAGELI

Parental  TQRELVSRQVSDDLTERAATFGLILDDVSLTHLTFGKEFTEAVEAKQVAQQEAERARFVVEKAEQQKKAA
          TQREL.SRQVSD.LTE.AATFGLILDDVSLTH.TFGKEFTEAVEAK.V.QQEAERARFVVEKAEQQK.AA
Retrocopy TQRELLSRQVSDNLTE*AATFGLILDDVSLTHPTFGKEFTEAVEAKEVDQQEAERARFVVEKAEQQKIAA

Parental  IISAEGDSKAAELIANSLATAGDGLIELRKLEAAEDIAYQLS-RSRNITYLP
          IISAE.DS.AA.LI.NSLATAGDGLIEL..LEAAEDI.YQLS..S.NITYLP
Retrocopy IISAEVDSMAAKLIPNSLATAGDGLIELSVLEAAEDITYQLS<SSENITYLP

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	0.02 RPM	74.79 RPM
SRP007412_cerebellum	0.00 RPM	61.05 RPM
SRP007412_heart	0.03 RPM	103.00 RPM
SRP007412_kidney	0.00 RPM	261.10 RPM
SRP007412_liver	0.00 RPM	155.59 RPM
SRP007412_testis	0.00 RPM	42.36 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3256 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3256 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3256 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4888
Gorilla gorilla	retro_ggor_3053
Pongo abelii	retro_pabe_3800
Callithrix jacchus	retro_cjac_4205

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 152 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004797	1 retrocopy	retro_acar_49,
Ailuropoda melanoleuca	ENSAMEG00000012364	1 retrocopy	retro_amel_258,
Bos taurus	ENSBTAG00000017120	1 retrocopy	retro_btau_481,
Canis familiaris	ENSCAFG00000016926	1 retrocopy	retro_cfam_202,
Choloepus hoffmanni	ENSCHOG00000007588	2 retrocopies	retro_chof_1159, retro_chof_2193,
Callithrix jacchus	ENSCJAG00000007174	22 retrocopies	retro_cjac_1048, retro_cjac_1403, retro_cjac_1683, retro_cjac_1761, retro_cjac_1820, retro_cjac_2261, retro_cjac_2389, retro_cjac_2390, retro_cjac_2391, retro_cjac_2445, retro_cjac_2523, retro_cjac_2659, retro_cjac_2663, retro_cjac_2909, retro_cjac_4205, retro_cjac_570, retro_cjac_635, retro_cjac_662, retro_cjac_872, retro_cjac_937, retro_cjac_966, retro_cjac_980,
Erinaceus europaeus	ENSEEUG00000006481	3 retrocopies	retro_eeur_219, retro_eeur_285, retro_eeur_369,
Homo sapiens	ENSG00000167085	15 retrocopies	retro_hsap_1113, retro_hsap_1514, retro_hsap_161, retro_hsap_1640, retro_hsap_2170, retro_hsap_2692, retro_hsap_3534, retro_hsap_3750, retro_hsap_3868, retro_hsap_3869, retro_hsap_4186, retro_hsap_4888, retro_hsap_517, retro_hsap_617, retro_hsap_776,
Gorilla gorilla	ENSGGOG00000028002	12 retrocopies	retro_ggor_124, retro_ggor_1722, retro_ggor_1876, retro_ggor_238, retro_ggor_2387, retro_ggor_246, retro_ggor_2607, retro_ggor_3053, retro_ggor_476, retro_ggor_643, retro_ggor_741, retro_ggor_870,
Macropus eugenii	ENSMEUG00000005122	1 retrocopy	retro_meug_708,
Microcebus murinus	ENSMICG00000006966	9 retrocopies	retro_mmur_1097, retro_mmur_1297, retro_mmur_1374, retro_mmur_1426, retro_mmur_1483, retro_mmur_1537, retro_mmur_1626, retro_mmur_62, retro_mmur_881,
Myotis lucifugus	ENSMLUG00000008203	2 retrocopies	retro_mluc_116, retro_mluc_2190,
Macaca mulatta	ENSMMUG00000000156	13 retrocopies	retro_mmul_1096, retro_mmul_1119, retro_mmul_1165, retro_mmul_1425, retro_mmul_151, retro_mmul_1565, retro_mmul_2148, retro_mmul_2420, retro_mmul_426, retro_mmul_521, retro_mmul_834, retro_mmul_866, retro_mmul_933,
Monodelphis domestica	ENSMODG00000012210	1 retrocopy	retro_mdom_812,
Nomascus leucogenys	ENSNLEG00000002978	13 retrocopies	retro_nleu_1190, retro_nleu_1254, retro_nleu_1326, retro_nleu_1557, retro_nleu_1755, retro_nleu_1796, retro_nleu_1874, retro_nleu_191, retro_nleu_195, retro_nleu_2547, retro_nleu_2573, retro_nleu_402, retro_nleu_444,
Oryctolagus cuniculus	ENSOCUG00000007209	1 retrocopy	retro_ocun_579,
Otolemur garnettii	ENSOGAG00000027015	1 retrocopy	retro_ogar_968,
Ochotona princeps	ENSOPRG00000000868	2 retrocopies	retro_opri_180, retro_opri_734,
Procavia capensis	ENSPCAG00000008851	1 retrocopy	retro_pcap_74,
Pongo abelii	ENSPPYG00000008920	16 retrocopies	retro_pabe_1262, retro_pabe_1357, retro_pabe_1409, retro_pabe_1770, retro_pabe_2291, retro_pabe_289, retro_pabe_3030, retro_pabe_3034, retro_pabe_3426, retro_pabe_3427, retro_pabe_3800, retro_pabe_552, retro_pabe_753, retro_pabe_922, retro_pabe_925, retro_pabe_977,
Pan troglodytes	ENSPTRG00000009376	14 retrocopies	retro_ptro_1025, retro_ptro_1110, retro_ptro_154, retro_ptro_1656, retro_ptro_1817, retro_ptro_2401, retro_ptro_2545, retro_ptro_2841, retro_ptro_2964, retro_ptro_3256 , retro_ptro_386, retro_ptro_451, retro_ptro_542, retro_ptro_686,
Rattus norvegicus	ENSRNOG00000046799	18 retrocopies	retro_rnor_1058, retro_rnor_1416, retro_rnor_1540, retro_rnor_1542, retro_rnor_2398, retro_rnor_2399, retro_rnor_2610, retro_rnor_2653, retro_rnor_2815, retro_rnor_2826, retro_rnor_2848, retro_rnor_2855, retro_rnor_2909, retro_rnor_292, retro_rnor_2948, retro_rnor_2949, retro_rnor_543, retro_rnor_898,
Ictidomys tridecemlineatus	ENSSTOG00000019929	2 retrocopies	retro_itri_337, retro_itri_945,