RetrogeneDB ID: retro_ptro_2393

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:140722084..140723484(+)
• 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_2393
GAAGCACAGTCTTTGAAGCAACAAGGAAATGCACACTATGCCAAGGAAGATTACAACGAAGCTTATAACTATTAGACAAA
AGCCACAGATATGTGCCCTAAAAATGCTAGCTATCATAGTAATAGAGCAGCTACATTGATGATACTTGGAAGGTTCTGCG
AAGCCCATGGAGATACTTTCACAGTGAAATTGGATGATGGTTTCTTCTGGGGACATCTATGAGAGGGCAAGTGCCACCTC
TCTCCAGGGAATGCCATGGCAGCACATTGCAGTTTTCAGAGAGCCCTAGAACTGGATCATAACAATGCTCACTCACAACA
GGAGTTCACAAATGCTAATGCAGTCAAGGAATAGGAGAAAGTCATAGAAACAAGTTTTGAGAAGTGGGCTTTTCAGAAGG
TTGTTTTCTGCATGGACTATGCCCTAGAATTTGCCCCTGTCTGCCATCACTTCAATATCCCTCAAAGCAGAATGTTTAGC
AATGCTGGATCGTTATCCAGAAGCACAGTCTGTGGCCAGTGATATTTTATGAACGGATTCCACCAATGTGGATGCTCTGT
ATGTATGCGGACTTTGCCTTTATTATGAAGATTGTATTGAGTAGGCAGTTGTTCAGTTTTTTGTGCAGGCTCTCAGAATG
GCTCCTGACCATGAGAAGGCCTGCCTTGCGTGCAGAAATACCAGAGCACTTCACGCAAAGAAAGAAGACTGGAATAAAGC
GTTTAGGGCAGGAAATTACAAACTAGCTGATGAACTGTACGCAGAATCCCCGGGGTAGACCCCGACAACATAAAAGCAAT
TGCTAAACTCTACTGTAACCGGGATATGGTTAATTCCGAGCTTGGGAAACTAGATGATGCAATAGACAGCTGCACAAATG
CAGTGAAGCTCATGACACTTACATAAAAGCCTACTTGAGAAGAGCTCAGTGTTTCTTGGACACAGAACAGTATGAAGAAA
CAGTGCGAGGCTATGAAAAAAGTATATCAGATGGAGAAAACAAAAGAATACAAACAGCTCCTAAAAAATGCACAGCTGGA
ACTGAAGAAGAGTAAGAGGGATAATTACTACAAGGTTCTGGAAGTGGACAAGAATGCCTCTGAGGACAAGATCAAGAAAG
CTTATTGGAAACAGGCCTTGAAGTACCATCCACATCGGCATGATGGAGCCAGCGCTGGGGTTCAAAAGGAGGAGGAGAAG
ATCAAGGAAGTGGCGAGGTCTTTATCATCCTCTTTGATTCCAAGAAAACGATTCATTATCACAGTGGACAGGACCTGGAT
AAGGAAGAAATAAATTTGGGTGATTTTGATGTAAACAATATCTTCAAGGTATTCTGCCGCGGTCCTACGGGCTTCAGCTG
TGAAGCATCTGGTCCAAGGAGTTTCTTTCTTCGATTGGGC

Alignment

ORF - retro_ptro_2393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.89 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EAETFKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDAQQSVRLDDSFV
          EA...K.QGNA.YAK.DYNEAYNY.TKA.DMCPKNASY..NRAATLM.LGRF.EA.GD....V.LDD.F.
Retrocopy EAQSLKQQGNAHYAKEDYNEAYNY*TKATDMCPKNASYHSNRAATLMILGRFCEAHGDTF-TVKLDDGFF

Parental  RGHLREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCMD
          .GHL.EGKCHLS.GNAMAA..SFQRALELDH.NA..QQEF.NANAV.E.EK..ET.FEK..F.KVVFCMD
Retrocopy WGHL*EGKCHLSPGNAMAAHCSFQRALELDHNNAHSQQEFTNANAVKE*EKVIETSFEKWAFQKVVFCMD

Parental  RALEFAPACHRFKI-LKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKA-VQFFV
          .ALEFAP.CH.F.I.LKAECLAML.RYPEAQSVASDIL..DSTN.DALYV.GLCLYYEDCIE.A.VQFFV
Retrocopy YALEFAPVCHHFNI>LKAECLAMLDRYPEAQSVASDIL*TDSTNVDALYVCGLCLYYEDCIE*AVVQFFV

Parental  QALRMAPDHEKACIACRNAKALKAKKEDGNKAFKEGNYKLAYELYTEA-LGIDPNNIKTNAKLYCNRGTV
          QALRMAPDHEKAC.ACRN..AL.AKKED.NKAF..GNYKLA.ELY.E...G.DP.NIK..AKLYCNR..V
Retrocopy QALRMAPDHEKACLACRNTRALHAKKEDWNKAFRAGNYKLADELYAES<PGVDPDNIKAIAKLYCNRDMV

Parental  NSKLRKLDDAIEDCTNAVKL-DDTYIKAYLRRAQCYMDTEQYEEAVRDYE-KVYQTEKTKEHKQLLKNAQ
          NS.L.KLDDAI..CTNAVKL..DTYIKAYLRRAQC..DTEQYEE.VR.YE.KVYQ.EKTKE.KQLLKNAQ
Retrocopy NSELGKLDDAIDSCTNAVKL<HDTYIKAYLRRAQCFLDTEQYEETVRGYE>KVYQMEKTKEYKQLLKNAQ

Parental  LELKKSKRKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQKEEEKKFKEV-GEAFTILSD
          LELKKSKR..YYK.L.VDKNASED.IKKAY.K.AL..HP.RH.GASA.VQKEEE.K.KEV.GE.F.IL.D
Retrocopy LELKKSKRDNYYKVLEVDKNASEDKIKKAYWKQALKYHPHRHDGASAGVQKEEE-KIKEV<GEVFIILFD

Parental  PKKKTRYDSGQDLDEEGMNMGDFDPNSIFKAFFGGPGGFSFEASGPGNFFFQFG
          .KK...Y.SGQDLD.E..N.GDFD.N.IFK.F..GP.GFS.EASGP..FF...G
Retrocopy SKKTIHYHSGQDLDKEEINLGDFDVNNIFKVFCRGPTGFSCEASGPRSFFLRLG

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	0.00 RPM	49.69 RPM
SRP007412_heart	0.09 RPM	53.28 RPM
SRP007412_kidney	0.00 RPM	45.35 RPM
SRP007412_liver	0.00 RPM	33.03 RPM
SRP007412_testis	0.11 RPM	70.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2393 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2393 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3524
Gorilla gorilla	retro_ggor_2382
Pongo abelii	retro_pabe_2911
Macaca mulatta	retro_mmul_1854

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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,