RetrogeneDB ID: retro_ptro_8

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:24635500..24637402(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000022593
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSPTRG00000000573
• Aliases: None
• Description: None

Sequence

>retro_ptro_8
ATGAACCCCAGCACCCCCAGCTACCCAACGGCCTCGCTGTACGTGGGGGACCTCCACCCCGACGTGACTGAGGCGATGCT
CTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACTTGATCACCCGCGGCTCCTCCAACT
ACGCGTATGTGAACTTCCAGCATCCGAAGGACGCGGAGCATGCTCTGGACACCATGAATTTTGATGTTATAAAGGGCAAG
CCACTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGAAAAAGTGGAATGGGCAACATATTCGTTAAAAATCTGGA
TAAATCCATTAATAATAAAGCACTGTATGATACAGTTTCTGCTTTTGGTAACATCCTTTCGTGTAACGTGGTTTGTGATG
AAAATGGTTCCAAGGGTTATGGATTTGTACACTTTGAGACACACGAAGCAGCTGAAAGAGCTATTGAAAAAATGAACGGA
ATGCTCCTAAATGGTCGCAAAGTATTTGTTGGACAATTTAAGTCTCGTAAAGAACGAGAAGCTGAACTTGGAGCTAGGGC
AAAAGAGTTCCCCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTTGGCAAGT
TCGGGCCCGCCTTAAGTGTGAAAGTAATGACCGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGG
CATGAAGATGCACAGAAAGCTGTAGATGAGATGAATGGAAAGGAGCTCAATGGAAAACAAATTTACGTTGGTCGAGCTCA
GAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCACATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGTTG
TTAATCTTTATGTGAAAAATCTTGATGATGATATTGATGATGAACGTCTCCAGAAAGCGTTTTCTCCATTTGGTACAATC
ACTAGTGCAAAGGTTATGATGGAAGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCAC
TAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGC
GCCAGGCTTACCTCACTAACGAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCAGCGAGCACCTCCTTCA
GGTTACTTCATGACAGCTGTCCCACAGACTCAGAACCATGCTGCATACTATCCTCCTAGCCAAATTACTCAACTAAGACC
AAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATAAGCCCAGTGCTATCCGCCCAGGTGCTCCTA
GAGTACCATTTAGTACTATGAGGCCAGCTTCTTCACAGATTCCACGAGTCATGTCAACGCAGCGTGTTGCTAACACATCA
ACACAGACAGTGGGTCCACGTCCTGCAGCTGCTGCTGCTGCTGCTGCTGCAGCTACCCCTGCTGTGCGCACGGTTGCACG
GTATAAATATGCTGCGGGAGTTCGCAATCCTCAGCAACATCTTAATGCACAGCCACAAGTTACAATGCAACAGCCTGCTG
TTCATGTACAAGGTCAGGAAACTTTGACTGCCTCCAGGTTGGCATCTGCCCCTCCTCAAAAGCAAAAGCAAATGTTAGGT
GAACGGCTCTTTCCTCTTATTCAAGCCATGCACCCTACTCTTGCTGGGAAAATCACTGGCATGTTGTTGGAGATTGATAA
TTCAGAACTTCTTTATATGCTCGAGTCTCCAGAGTCACTCCGTTCTAAGGTTGATGAAGCTGTAGCTGTACTACAAGCCC
ACCAAGCTAAAGAGGCTACCCAGAAAGCAGTTAACAGTGCTACCGGTGTTCCAACTGTTTAA

Alignment

ORF - retro_ptro_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.93 %
• Parental protein coverage: 59.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN....SYP.ASLYVGDLH.DVTEAMLYEKFSPAGP.LSIRVCRD.ITR.S..YAYVNFQ.P.DAE.ALD
Retrocopy MNPSTPSYPTASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDLITRGSSNYAYVNFQHPKDAEHALD

Parental  TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGKP.RIMWSQRDPSLRKSG.GN.F.KNLDKSI.NKALYDT.SAFGNILSC.VVCDENGSKGY
Retrocopy TMNFDVIKGKPLRIMWSQRDPSLRKSGMGNIFVKNLDKSINNKALYDTVSAFGNILSCNVVCDENGSKGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL
          .FVHFET.EAA..AIEKMNGMLLN.RKVFVG.FKSRKEREAELGA.AKEF.NVYIKNFGE..DDE.LK.L
Retrocopy GFVHFETHEAAERAIEKMNGMLLNGRKVFVGQFKSRKEREAELGARAKEFPNVYIKNFGEDMDDERLKDL

Parental  FSQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKF
          F..FG..LSVKVM.D..GKSKGFGFVS.E.HEDA.KAV.EMNGKE..GK.I.VGRAQKKVERQ.ELKR.F
Retrocopy FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRTF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQ.KQ.RI.RYQ.VNLY.KNLDD.IDDE.L.K.FSPFG.ITSAKVM.E.GRSKGFGFVCFSSPEEATKAV
Retrocopy EQMKQDRITRYQVVNLYVKNLDDDIDDERLQKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALP
          TEMNGRIV..KPLYVALAQRKEER.A.LTN.YMQR.A..RA.P
Retrocopy TEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQRMASVRAVP

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	2.88 RPM	36.46 RPM
SRP007412_cerebellum	6.02 RPM	42.12 RPM
SRP007412_heart	4.31 RPM	70.36 RPM
SRP007412_kidney	7.40 RPM	55.44 RPM
SRP007412_liver	9.30 RPM	63.60 RPM
SRP007412_testis	637.78 RPM	84.94 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_ptro_8 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DC528021	24635716	24636138	96.2	403	16	387
DC528717	24635529	24636203	95.2	641	33	608

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_8 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_8 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_88
Pongo abelii	retro_pabe_68

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8 ,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pan troglodytes	ENSPTRG00000014709	1 retrocopy	retro_ptro_16,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,