RetrogeneDB ID: retro_ptro_40

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:31246596..31247403(+)
• Located in intron of: ENSPTRG00000003470

Retrocopy information

• Ensembl ID: ENSPTRG00000001248
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ANP32B
• Ensembl ID: ENSPTRG00000021172
• Aliases: None
• Description: None

Sequence

>retro_ptro_40
ATGGAGATGAAGAAGAAGATTAACCTGGAGTTAAGGAACAGATCCCCGGAGGAGGTGACAGAGTTAGTCCTTGATAATTG
CCTATGTGTCAATGGGGAAATTGAAGGCCTGAATGATACTTTCAAAGAACTAGAATTTCTGAGTATGGCTAATGTGGAAC
TAAGTTCGCTGGCCCGGCTTCCCAGCTTAAATAAACTTCGAAAATTGGAGCTTAGTGATAATATAATTTCTGGAGGCTTG
GAAGTCCTAGCAGAGAAATGTCCAAATCTTACCTACCTCAATCTGAGTGGAAACAAAATAAAAGATCTCAGTACAGTAGA
AGCTCTGCAAAATCTTAAAAATTTGAAAAGTCTTGACCTGTTTAACTGTGAGATCACAAACCTGGAAGATTATAGAGAAA
GTATTTTTGAACTGCTGCAGCAAATCACATACTTAGATGGATTTGATCAGGAGGATAATGAAGCGCCGGACTCTGAAGAG
GAGGATGATGAGGATGGAGATGAAGATGATGAAGAGGAAGAGGAAAATGAAGCTGGTCCACCGGAAGGATATGAGGAAGA
GGAGGAGGAAGAGGAAGAGGAGGATGAGGATGAGGATGAAGATGAAGATGAAGCAGGTTCAGAGTTGGGAGAGGGAGAAG
AGGAAGTGGGCCTCTCATACTTAATGAAAGAAGAAATTCAGGATGAAGAAGATGATGATGACTATGTTGAAGAAGGGGAA
GAAGAGGAGGAAGAGGAAGAAGGAGGTCTTCGAGGGGAGAAGAGGAAACGAGATGCTGAAGACGATGGAGAGGAAGAAGA
TGACTAG

Alignment

ORF - retro_ptro_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.85 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDMKRRIHLELRNRTPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSNLPKLPKLKKLE
          M.MK..I.LELRNR.P..V.ELVLDNC....G.IEGL...F..LEFLS..NV.L.S...LP.L.KL.KLE
Retrocopy MEMKKKINLELRNRSPEEVTELVLDNCLCVNGEIEGLNDTFKELEFLSMANVELSSLARLPSLNKLRKLE

Parental  LSENRIFGGLDMLAEKLPNLTHLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVTNLNDYRESVFKLLP
          LS.N.I.GGL..LAEK.PNLT.LNLSGNK.KD.ST.E.L..L..LKSLDLFNCE.TNL.DYRES.F.LL.
Retrocopy LSDNIISGGLEVLAEKCPNLTYLNLSGNKIKDLSTVEALQNLKNLKSLDLFNCEITNLEDYRESIFELLQ

Parental  QLTYLDGYDREDQEAPDSDAEVDGVDEEEEDEEGEDEEDEEDEDGEEEEFDEEDDEDEDVEGDEDDDEVS
          Q.TYLDG.D.ED.EAPDS..E.D....E...EE.E.E........EEEE..EE.DEDED...DE...E..
Retrocopy QITYLDGFDQEDNEAPDSEEEDDEDGDEDDEEEEENEAGPPEGYEEEEEEEEEEDEDEDEDEDEAGSELG

Parental  EEEEEFGLDEEDEDEDEDEEEEEGGKGEKRKRETDDEG
          E.EEE.GL......E..DEE.......E....E...EG
Retrocopy EGEEEVGLSYLMKEEIQDEEDDDDYVEEGEEEEEEEEG

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	7.47 RPM	36.00 RPM
SRP007412_cerebellum	34.34 RPM	40.58 RPM
SRP007412_heart	15.10 RPM	54.12 RPM
SRP007412_kidney	9.47 RPM	55.89 RPM
SRP007412_liver	5.47 RPM	94.86 RPM
SRP007412_testis	3.37 RPM	78.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_40 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_40 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005149	6 retrocopies	retro_chof_1293, retro_chof_1456, retro_chof_19, retro_chof_2244, retro_chof_588, retro_chof_681,
Cavia porcellus	ENSCPOG00000020118	3 retrocopies	retro_cpor_1336, retro_cpor_493, retro_cpor_509,
Equus caballus	ENSECAG00000012310	2 retrocopies	retro_ecab_246, retro_ecab_826,
Echinops telfairi	ENSETEG00000015514	4 retrocopies	retro_etel_2053, retro_etel_2167, retro_etel_510, retro_etel_677,
Homo sapiens	ENSG00000136938	2 retrocopies	retro_hsap_1597, retro_hsap_1603,
Myotis lucifugus	ENSMLUG00000004844	2 retrocopies	retro_mluc_1787, retro_mluc_1788,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Monodelphis domestica	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
Mustela putorius furo	ENSMPUG00000006433	1 retrocopy	retro_mputfur_1392,
Mus musculus	ENSMUSG00000028333	1 retrocopy	retro_mmus_2399,
Nomascus leucogenys	ENSNLEG00000016941	1 retrocopy	retro_nleu_3009,
Otolemur garnettii	ENSOGAG00000006091	2 retrocopies	retro_ogar_1915, retro_ogar_3282,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Pan troglodytes	ENSPTRG00000021172	3 retrocopies	retro_ptro_1073, retro_ptro_1075, retro_ptro_40 ,
Pteropus vampyrus	ENSPVAG00000006569	1 retrocopy	retro_pvam_699,
Sorex araneus	ENSSARG00000000804	1 retrocopy	retro_sara_549,
Tupaia belangeri	ENSTBEG00000002189	8 retrocopies	retro_tbel_1659, retro_tbel_2710, retro_tbel_2772, retro_tbel_3770, retro_tbel_3863, retro_tbel_4351, retro_tbel_4361, retro_tbel_491,
Tursiops truncatus	ENSTTRG00000010825	2 retrocopies	retro_ttru_1899, retro_ttru_341,