RetrogeneDB ID: retro_ptro_304

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:63946432..63947541(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSPTRG00000009188
• Aliases: None
• Description: None

Sequence

>retro_ptro_304
AGTTTCCAGAGAGCCCTAGAACTGGATCATAAAAATGCTCAGGAATAACAGGAGTTCAAGAATGCCAATTCAATAATGGA
ATATGAGAAGTTAGCAAAAACAGATTTTGAGAAGCATGATATTAGGAAGGTTGTTCTCTGCATGGACTGTGCCCGAGCAC
TTGCCCCTTGCCTGCCATTGCTTCAAAATCCTCAAAGCAGAATATTTAGTAATGCTGGGTCATTATCCAGAAGCACAATC
TGTGGCCAGTGACATTTTACAAATGGAGTCCACCAATGCAGATCCTCTGTATGTATAAGGTCTTTGCCTTTATTATGAAG
ATTGTATTGACAAGTCAGTTCAGTTTTTGTATAGGCTCTTAGGATGGCTCCATGAGAGGGCCTGCGTTGCTTGCAGAAAT
CCCAAAGCACTCAAAGCAAAGAAAGAAGACAGAAATAAAGCATTTAAGGAAGGAAATTACAAGCTAGCATACGAACTGTA
CACATGACCCCTGGGGATAAACCCCAACAATATAAAAACTAAGCTAAACTCTACTATAATTGGGTTATGGTTAATTCTAA
GCTTAGGAAACTAGATAATGCAATACAAGACTGCACAAATACAGTGAAGCTCAATGACACCTATTTAAAAGCCTGCTTGA
GAAGAGCTCAGTGTTACATGAACACCAAACAGTATGAAGAAGCAGTGCACAATTATGAAAAAGTGTATCAGACAGAGAAA
ACAAAAGAACAAAAACAGCTCCTAAAAAATGCACAGCTGAAACTGAAGAAGAGTAAGAAGAAAGATTACTACAAGATTCT
GGGAGTGGACAATAATGCCTCTGAGGACGAGACCAAGAAAGCTTATCACAAATGGGCCTTGATGCACCATCCAGATTGGC
ACAGTGGAGGCAGTGCTGAGGTTCAGAAGGAGGAGGGAAAGTTCAAGGAAATTGGAGAGGCCTTTACCATCTTCTCTGAT
CCCAAGAAAAAGACTCGCTAGGACAGTGGACAGGACCTGGACAAGGAGGGCATGAATATGGGTGATTTTGATGCAAATAG
TATCTTCAAGGCATTCTTCAGTGGTCTTGGGGCTTCAGCTTTGAAGCGTCTGGTCCAGGGAATTTTTTT

Alignment

ORF - retro_ptro_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.05 %
• Parental protein coverage: 75.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCMDRALEFAP-ACHRFKILKAECL
          SFQRALELDHKNAQ..QEFKNAN..MEYEK.A.TDFEK.D.RKVV.CMD.A...AP.ACH.FKILKAE.L
Retrocopy SFQRALELDHKNAQE*QEFKNANSIMEYEKLAKTDFEKHDIRKVVLCMDCARALAP>ACHCFKILKAEYL

Parental  AMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKAVQFFVQALRMAPDHEKACIACRNAKAL
          .MLG.YPEAQSVASDIL.M.STNAD.LYV.GLCLYYEDCI.K.VQF....L.....HE.AC.ACRN.KAL
Retrocopy VMLGHYPEAQSVASDILQMESTNADPLYV*GLCLYYEDCIDKSVQFLYRLLGWL--HERACVACRNPKAL

Parental  KAKKEDGNKAFKEGNYKLAYELYTEALGIDPNNIKTN-AKLYCNRGTVNSKLRKLDDAIEDCTNAVKLDD
          KAKKED.NKAFKEGNYKLAYELYT..LGI.PNNIKT..AKLY.N...VNSKLRKLD.AI.DCTN.VKL.D
Retrocopy KAKKEDRNKAFKEGNYKLAYELYT*PLGINPNNIKTK<AKLYYNWVMVNSKLRKLDNAIQDCTNTVKLND

Parental  TYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLELKKSKRKDYYKILGVDKNASED
          TY.KA.LRRAQCYM.T.QYEEAV..YEKVYQTEKTKE.KQLLKNAQL.LKKSK.KDYYKILGVD.NASED
Retrocopy TYLKACLRRAQCYMNTKQYEEAVHNYEKVYQTEKTKEQKQLLKNAQLKLKKSKKKDYYKILGVDNNASED

Parental  EIKKAYRKRALMHHPDRHSGASAEVQKEEEKKFKEVGEAFTILSDPKKKTRYDSGQDLDEEGMNMGDFDP
          E.KKAY.K.ALMHHPD.HSG.SAEVQK.EE.KFKE.GEAFTI.SDPKKKTR.DSGQDLD.EGMNMGDFD.
Retrocopy ETKKAYHKWALMHHPDWHSGGSAEVQK-EEGKFKEIGEAFTIFSDPKKKTR*DSGQDLDKEGMNMGDFDA

Parental  NSIFKAFFGGPG-GFSFEASGPGNFF
          NSIFKAFF.G.G.GFSFEASGPGNFF
Retrocopy NSIFKAFFSGLG<GFSFEASGPGNFF

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	50.48 RPM
SRP007412_cerebellum	0.04 RPM	49.69 RPM
SRP007412_heart	0.00 RPM	53.28 RPM
SRP007412_kidney	0.00 RPM	45.35 RPM
SRP007412_liver	0.00 RPM	33.03 RPM
SRP007412_testis	0.00 RPM	70.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_304 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_304 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_398
Pongo abelii	retro_pabe_317
Macaca mulatta	retro_mmul_501

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569, retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304 ,