RetrogeneDB ID: retro_ptro_1286

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:18095939..18097985(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040575
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CTAGE5
• Ensembl ID: ENSPTRG00000006297
• Aliases: None
• Description: None

Sequence

>retro_ptro_1286
ACAGAAGCACAAAGTTTGGAGGCAACCTGCGAAAAGCTGAACAGGTTCAATTCTGAACTTGTGCATGAAATACTCTGTCT
AGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTGAACAAAATGAATTGATGGCGGATATTTCCAAAAGGATACAGT
CGCTAGAAGATGAGTCAAAATCCCTCAAATCACAAGTAGCTGAAGCCAAAATGACCTTCAAGAGATTTCAAGCGAATGAA
GAACGATTGGAGATAGAAATACAAGATGCTTGGAATGAAAATTCTGAACTTCAGGCAAGCCAGAAACAGCTTTTGCAAGA
AGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTATTAAACAGAAAAGAACATTTGAAGACTCAAAAGTACATGCAGAAC
AAGTTCTAAATGATAAAGAAAATCACATCAAGACTCTGACTGAACGCTTGCTAAAGATGAAAGATGGGGTTGCTATGCCT
GAAGAAGATGTAACGGATCATGATAACTTGGAATTAGAAATGAACAGTGAATCGGAAGATGGTGCTTACTTAGATAATCC
TCCAAAAGGAGCTTTGAAGAAACTGATTCATACTGCTAAGTTAAATGCTTCCTTAAAAACCTTAGAAGGAGAAAGAAACC
AAATTTATATTCAATTATCTGAAGTTGATAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTGAACAA
GCATCTTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAGCAGAAACTTAAAGTAATGACTGAATT
ATATCAAGAAAATAAAATGAAACTCTACAGGAAATTAATAGTAGAGGAAAAATGCCGGTTAGAGAAAGAAGAGAAACTTT
CTAAAGTAGACGAAATGATCAGCCATGCCACTGAAGAGCTGGAGACCTACCGAAAGCGAGCCAAAGATCTTAAAGAATTT
GAGAGAACTATTCATTTTTATCAAAAGAAGATTATTCTCCATGAGAAAAAAGCACATGATAATTGGTCGGCAGCTTGGAC
TGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAACTGAAATAGAGTTTAAAATAA
AACTTTTAGGAAAAGATCCTTATGGACTTGACGTTCCAAATACAGCATTTGGCAGACAGCATTCCCCATATGGTCCCTCA
CCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTCTCTCTATCCTCCAACTTTGTTGGAAGGTCCTCTCAGACTCTCACC
TTTGCTTCCACGGGGAGGAGGAAGAGGCTCCAGAGGCCCAGGGAATCCTCCGGACCATCAGATTACCAAACAAAGAGGAG
AATCAAGCTGTGATAGGTTAACTGATCCTCACAGGGCTCCTTCTGACGCTGGGCCCCTGTCACCTCCGTGGGAACAGGAC
TGTAGGATGATGTTTCCTCCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGGCAGATTTTATTC
TAATTGTGCTAGACTCTCTGGACCAGCAGAACTCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGC
CTTCAGAAATGGAATCCAGTAGAAATGATACCAAAGATAATCTTGGTAATTTAAAGGTGCCTGATTCATCTCTCCCCGCT
GAAAATGAAGCAACTGGCCCTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTTTATTGTTTCCAGTGGATACGAG
GGGCCCGTTCATGAGGAGAGGACCTCCTTTCCCCCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTC
CTCCAAGGGATGCCCCAGGTCCACCACGTGCTCCATTTGCAATGAGAAATGTCTACCTACCGAGAGGTTTTCTTCCTTAC
CGTCCCCCAAGACCTGCATTTTTCCCCCCAGCCCCCACATTCTGAAGGTAGAATGAGTTTCCATCAGGGTTGAGTCCGAC
TTCAAATGAGCCTGCTGCTGAACATCCAGAACGACAGCAAGAAACC

Alignment

ORF - retro_ptro_1286 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.74 %
• Parental protein coverage: 84.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKRIQSLEDESKSLKSQVAEAK
          TEAQSLEATCEKLNR.NSEL..EILCLEKELKEEKSKHSE..ELMADISKRIQSLEDESKSLKSQVAEAK
Retrocopy TEAQSLEATCEKLNRFNSELVHEILCLEKELKEEKSKHSEQNELMADISKRIQSLEDESKSLKSQVAEAK

Parental  MTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSEVHAEQVLNDKE
          MTFK.FQ.NEERL.I.I.DA.NENS.LQ.SQKQLLQEAEVWKEQVSEL.KQK.TFEDS.VHAEQVLNDKE
Retrocopy MTFKRFQANEERLEIEIQDAWNENSELQASQKQLLQEAEVWKEQVSELIKQKRTFEDSKVHAEQVLNDKE

Parental  SHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEG
          .HIKTLTERLLKMKD..AM..ED.TD.DNLELEMNSESE.GAYLDNPPKGALKKLIH.AKLNASLKTLEG
Retrocopy NHIKTLTERLLKMKDGVAMPEEDVTDHDNLELEMNSESEDGAYLDNPPKGALKKLIHTAKLNASLKTLEG

Parental  ERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLT
          ERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFE.ENQKLQQKLKVMTELYQEN.MKL.RKL.
Retrocopy ERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFESENQKLQQKLKVMTELYQENKMKLYRKLI

Parental  VEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWLAARNAE
          VEE..RLEKEEKLSKVDE.ISHATEELETYRKRAKDL.E..ERTIH.YQ..II.HEKKAHDNW.AA..AE
Retrocopy VEEKCRLEKEEKLSKVDEMISHATEELETYRKRAKDLKE-FERTIHFYQKKIILHEKKAHDNWSAAWTAE

Parental  RNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTLL
          RNLNDLRKENAHNRQKLTE.E.K..LL.KDPY.LDVPNTAFGR.HSPYGPSPLG.PSSETRA.L.PPTLL
Retrocopy RNLNDLRKENAHNRQKLTEIEFKIKLLGKDPYGLDVPNTAFGRQHSPYGPSPLGRPSSETRASLYPPTLL

Parental  EGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPPG
          EGPLRLSPLLP.GGGRGSRGPGNP.DHQIT..RGESSCDRLTDPHRAPSD.G.LSPPW.QD.RMMFPPPG
Retrocopy EGPLRLSPLLPRGGGRGSRGPGNPPDHQITKQRGESSCDRLTDPHRAPSDAGPLSPPWEQDCRMMFPPPG

Parental  QSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSLP
          QSYPDSALPPQRQ.RF.SN..RLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKD.LGNL.VPDSSLP
Retrocopy QSYPDSALPPQRQGRFYSNCARLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDNLGNLKVPDSSLP

Parental  AENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPPAPFAMR
          AENEATGPGFVPPPLAPIRG.LFPVDTRG.F.RRGPPFPPPPPG.MFGAS.DYFPPRD.PGPP.APFAMR
Retrocopy AENEATGPGFVPPPLAPIRGLLFPVDTRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDAPGPPRAPFAMR

Parental  NVYPPRGFPPYLPPRPGFFPP-PPHSEGR-SEFPSGLIPPSNEPATEHPEPQQET
          NVY.PRGF.PY.PPRP.FFPP.PPHSEGR..EFPSGL.P.SNEPA.EHPE.QQET
Retrocopy NVYLPRGFLPYRPPRPAFFPP>PPHSEGR<NEFPSGLSPTSNEPAAEHPERQQET

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	0.00 RPM	10.90 RPM
SRP007412_cerebellum	0.00 RPM	9.86 RPM
SRP007412_heart	0.00 RPM	11.02 RPM
SRP007412_kidney	0.00 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	9.91 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1286 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1286 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1286 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_78
Pongo abelii	retro_pabe_1588

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286 , retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,