RetrogeneDB ID: retro_ptro_2253

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:40774542..40775591(-)
• Located in intron of: ENSPTRG00000016991

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1A
• Ensembl ID: ENSPTRG00000033819
• Aliases: None
• Description: None

Sequence

>retro_ptro_2253
ATGTCACTGCATCAGTTTTTACTAGAGCCAATCAACTGTCGTGCCTGAAACAGGGATCGTACCCAGATTGCCCTCAGTGT
CAATAATCACGAAGTGCACATCTATAAGAAGAATGGGCACCAGTGTGTGAAAGCTCACGAACTCAAGGAGCACAATGGAC
ACATCACAGATATTGACTGGGCTCCCAAGAGTGACCACATCGTCACTTGTGGGGCAGACCACAATGCCTATGTCTGGAGT
CAGAAAGATGGTGTCTGGAAGCCAACACTGATCATCCTGAGAATTAATCGCACAGCTACTTTTGTGAAGTGGTCCGCCCT
AAAGAACAAATTTGCTGTGGGAAGTGAAGCACGACTCATTTCAGTTTGTTACTTTGAGTCTGAAAATGCCTGGTGGGTGA
GCAAGCACATTAAAAAGCTGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATCCCAACAATGTTTTGCTAGCAGCAGGA
TCATGTGACTTCAAACACAGAGTGTTTTCTTCCTACATTAAAGAAGTGGATGAAAAGCTGGCCAGCATGCCCTGGGACAG
CAAGATGCCTTTTGGGCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGTGGCTGGGTCCACGGGGTCAGCTTCTCCG
CCAGTGGGAGCCACCTGGTCTGGGCCAGCCACGACAGCACCATGTCTGCTGCTGATGCCTCAAAAAGTGTGCATGTCTCA
ATCTGAAGACGGAGTTCCAGCTGCTCCTGAGTGTGTCGTCTGTCTCACACAACAGCGCCGTGGCTGCTGGCCATGACTGC
TGACCAATGCTCTTGAACTACGATGACCGTGGCTGCCTGACCTTTGTCTCCAAGTTAGACTTTCCAAAACAGAGCATCCA
ACGCAACATGTCTGCCATGGAATGCTTCTGCAACATGGACAAGAGGGCCACGACTGAGGGCTGCAACATGGCTTTGAAGA
TGCTGCACCAGAATAGCATCACTCAAGTCTCTATTTATGAGGTGGACGAGAAAGATTGTCGCAAATATTGCACTACTGGC
ATCGATGGA

Alignment

ORF - retro_ptro_2253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 94.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWVKAHELKEHNGHITGIDWAPKSDRIVTC
          MSLHQFLLEPI.C.A.NRDRTQIALS.NNHEVHIYKKNG.Q.VKAHELKEHNGHIT.IDWAPKSD.IVTC
Retrocopy MSLHQFLLEPINCRA*NRDRTQIALSVNNHEVHIYKKNGHQCVKAHELKEHNGHITDIDWAPKSDHIVTC

Parental  GADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKKP
          GAD.NAYVWSQKDGVWKPTL.ILRINR.ATFVKWS.L.NKFAVGS.ARLISVCYFESEN.WWVSKHIKK.
Retrocopy GADHNAYVWSQKDGVWKPTLIILRINRTATFVKWSALKNKFAVGSEARLISVCYFESENAWWVSKHIKKL

Parental  IRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASTPWGSKMPFGQLMSEFGGSGTGGWVHGV
          IRSTVLSLDWHPNNVLLAAGSCDFK.RVFS.YIKEVDEK.AS.PW.SKMPFGQLMSEFGGSGTGGWVHGV
Retrocopy IRSTVLSLDWHPNNVLLAAGSCDFKHRVFSSYIKEVDEKLASMPWDSKMPFGQLMSEFGGSGTGGWVHGV

Parental  SFSASGSRLAWVSHDSTVSVADASKSVQVS-TLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGC
          SFSASGS.L.W.SHDST.S.ADASKSV.VS..LKTEF..LLSVS.VS.NS.VAAGHDC.PML.NYDDRGC
Retrocopy SFSASGSHLVWASHDSTMSAADASKSVHVS<NLKTEFQLLLSVSSVSHNSAVAAGHDC*PMLLNYDDRGC

Parental  LTFVSKLDIPKQSIQRNMSAMERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGID
          LTFVSKLD.PKQSIQRNMSAME.F.NMDKRATTE..N.AL..LHQNSITQVSIYEVD..DCRK.CTTGID
Retrocopy LTFVSKLDFPKQSIQRNMSAMECFCNMDKRATTEGCNMALKMLHQNSITQVSIYEVDEKDCRKYCTTGID

Parental  G
          G
Retrocopy G

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	81.60 RPM
SRP007412_cerebellum	0.14 RPM	45.78 RPM
SRP007412_heart	0.00 RPM	47.51 RPM
SRP007412_kidney	0.03 RPM	62.29 RPM
SRP007412_liver	0.00 RPM	39.02 RPM
SRP007412_testis	0.21 RPM	49.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2253 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2253 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3191
Gorilla gorilla	retro_ggor_1337
Pongo abelii	retro_pabe_2647
Macaca mulatta	retro_mmul_2012

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006322	1 retrocopy	retro_amel_1431,
Bos taurus	ENSBTAG00000004242	1 retrocopy	retro_btau_1486,
Callithrix jacchus	ENSCJAG00000015859	3 retrocopies	retro_cjac_2141, retro_cjac_2165, retro_cjac_2263,
Cavia porcellus	ENSCPOG00000001777	2 retrocopies	retro_cpor_452, retro_cpor_981,
Dipodomys ordii	ENSDORG00000016059	1 retrocopy	retro_dord_593,
Equus caballus	ENSECAG00000016467	1 retrocopy	retro_ecab_185,
Homo sapiens	ENSG00000241685	2 retrocopies	retro_hsap_2010, retro_hsap_3191,
Loxodonta africana	ENSLAFG00000014024	1 retrocopy	retro_lafr_1006,
Macropus eugenii	ENSMEUG00000005609	8 retrocopies	retro_meug_1033, retro_meug_1081, retro_meug_1495, retro_meug_1668, retro_meug_1755, retro_meug_1912, retro_meug_2179, retro_meug_492,
Myotis lucifugus	ENSMLUG00000010912	1 retrocopy	retro_mluc_1432,
Macaca mulatta	ENSMMUG00000019342	2 retrocopies	retro_mmul_1383, retro_mmul_2012,
Monodelphis domestica	ENSMODG00000001303	9 retrocopies	retro_mdom_1360, retro_mdom_1380, retro_mdom_1438, retro_mdom_1551, retro_mdom_1796, retro_mdom_1917, retro_mdom_686, retro_mdom_699, retro_mdom_808,
Mus musculus	ENSMUSG00000029621	1 retrocopy	retro_mmus_1373,
Nomascus leucogenys	ENSNLEG00000010852	2 retrocopies	retro_nleu_1663, retro_nleu_2069,
Oryctolagus cuniculus	ENSOCUG00000003944	1 retrocopy	retro_ocun_1130,
Otolemur garnettii	ENSOGAG00000010870	6 retrocopies	retro_ogar_1547, retro_ogar_2690, retro_ogar_2697, retro_ogar_381, retro_ogar_610, retro_ogar_656,
Pongo abelii	ENSPPYG00000025816	4 retrocopies	retro_pabe_1647, retro_pabe_1648, retro_pabe_2537, retro_pabe_2647,
Pan troglodytes	ENSPTRG00000033819	2 retrocopies	retro_ptro_1340, retro_ptro_2253 ,
Sarcophilus harrisii	ENSSHAG00000010673	2 retrocopies	retro_shar_180, retro_shar_727,
Ictidomys tridecemlineatus	ENSSTOG00000001660	1 retrocopy	retro_itri_1834,
Tupaia belangeri	ENSTBEG00000011381	3 retrocopies	retro_tbel_1237, retro_tbel_1241, retro_tbel_82,