RetrogeneDB ID: retro_ptro_668

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:11763542..11764681(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX55
• Ensembl ID: ENSPTRG00000005601
• Aliases: None
• Description: None

Sequence

>retro_ptro_668
TCTCCTCTGTTCCAAGTTTAAGAGTTTAAGCAACAAGGTGGGAACATCACTGTGGCCATTCCAGGCCACTTGAAGACAGG
TTCTGAAGGAAGGCAGAAGGCTTGTATCTGGCCAGCTGTGTGTGATCCCTGCATATCCTGGTGTTGGATGAGGCAGACAG
ACTTCTGGACATGGGATTTGAGGCAAGCATAAATACCATCCTGGAGTTTTTGCCAAAGCAGAGGAGAACAGGCCTTTTCT
CTGCCACTCAGAAGCAGGAAGTGGAGAACTTGGGGAGAGTGGGACGCCGGAACCCTGTCCAGTCTCAGTGAAGAAGGGTG
TGGCAGCCAGCAGTGCCCAGAACACCACTCTCCCCTAGAAAACTACTACATGGTATGCAAGGCAGATGAGAAATTTAATC
AGCTGCTACATTTTCTTCGCAGTCATAAGCAAGAGCAACACCTGGTCTTCTTTAGCACCTGCACCTGTGTGGAATACTAC
AGGAAGGCTCTGGAGGTGCTGATGAAGAGTGTGAAGATTGTGTGCATCCATGGAAAGATGAAATACGATCTTCATGCAAA
TTGAAAATTGCAATTGTTCTGCAAATTGCAAAGTGGAATTTTAGTGTGCACTGATGTGGTGGCCCAGGAATCAATGTTCC
TGAAGTAAACTGGGTTTTGCAGTACAATCGCCCCTACAATGCAAGTGCCTTTGTGCAGCACTGTAGCCGCACAGCCCTCA
TTGGCCACAGAGGCAGAGCTCTGGTGTTCCTCCCGCCCGTGGAAGAGTCATACATCAATTTCCTTGCAATTAACCAAAAA
TGCCCCCTGGCGGAGATGAAACTCTAGAAAAACACAGCTGACCTTCTGCCAAAACTCAAGTCCATGACCCTGGCAGAAAC
ATCTGTGTTTGAAAAGGGCATGAAAGCTTTTGTGTCCTATGTCCAGGCTTATGCAAAGTAAGAATGCAACCTGATTTTCA
GATTAAATAATCTTGATTTTGCAAGTCTTGCTCGAGGTTTTTCCCTGCTGAGAATGCCCAAGATGCCAGAATTGAGAGGA
AAGCAGTTTCCAGATTTTGTGCCTGTGGACATTAATACAGACACTATTTCATTTAAAGATAAAATTAGAGAAAAGCAGAG
GCAGAAATTACTGGAGCAA

Alignment

ORF - retro_ptro_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 63.33 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NPGEDVEKFKQQGGNIIVATPGRL-EDMFRRKAEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILE
          .P...V..FKQQGGNI.VA.PG.L.ED.F.RKAEGL.LASCV.SL..LVLDEADRLLDMGFEASINTILE
Retrocopy SPLFQV*EFKQQGGNITVAIPGHL<EDRF*RKAEGLYLASCV*SLHILVLDEADRLLDMGFEASINTILE

Parental  FLPKQRRTGLFSATQTQEVENLVRAGLRNPVR-VSVKEKGVAASSAQKTP-SRLENYYMVCKADEKFNQL
          FLPKQRRTGLFSATQ.QEVENL.R.G.RNPV..VSVK.KGVAASSAQ.T..S.LENYYMVCKADEKFNQL
Retrocopy FLPKQRRTGLFSATQKQEVENLGRVGRRNPVQ<VSVK-KGVAASSAQNTT<SPLENYYMVCKADEKFNQL

Parental  VHFLRNHKQEKHLVFFSTCACVEYYGKALEVLVKGVKIMCIHG--KMKYKRNKIFMEFRKLQSGILVCTD
          .HFLR.HKQE.HLVFFSTC.CVEYY.KALEVL.K.VKI.CIHG..K.....N.....F.KLQSGILVCTD
Retrocopy LHFLRSHKQEQHLVFFSTCTCVEYYRKALEVLMKSVKIVCIHGKMKYDLHAN*KLQLFCKLQSGILVCTD

Parental  VMAR-GIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHGGSALVFLLPMEESYINFLAINQKCPLQEMK
          V.A..GI..PEVNWVLQY..P.NASAFV..C.RTA.IGH.G.ALVFL.P.EESYINFLAINQKCPL.EMK
Retrocopy VVAQ<GINVPEVNWVLQYNRPYNASAFVQHCSRTALIGHRGRALVFLPPVEESYINFLAINQKCPLAEMK

Parental  PQRNTADLLPKLKSMALADRAVFEKGMKAFVSYVQAYAKHECNLIFRLKDLDFASLAQGFALLRMPKMPE
          ...NTADLLPKLKSM.LA...VFEKGMKAFVSYVQAYAK.ECNLIFRL..LDFASLA.GF.LLRMPKMPE
Retrocopy L*KNTADLLPKLKSMTLAETSVFEKGMKAFVSYVQAYAK*ECNLIFRLNNLDFASLARGFSLLRMPKMPE

Parental  LRGKQFPDFVPVDVNTDTIPFKDKIREKQRQKLLEQ
          LRGKQFPDFVPVD.NTDTI.FKDKIREKQRQKLLEQ
Retrocopy LRGKQFPDFVPVDINTDTISFKDKIREKQRQKLLEQ

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	0.91 RPM	7.27 RPM
SRP007412_cerebellum	0.07 RPM	20.36 RPM
SRP007412_heart	0.03 RPM	3.03 RPM
SRP007412_kidney	0.00 RPM	8.05 RPM
SRP007412_liver	0.03 RPM	8.51 RPM
SRP007412_testis	0.00 RPM	9.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_668 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_668 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_964

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000111364	1 retrocopy	retro_hsap_964,
Gorilla gorilla	ENSGGOG00000026102	1 retrocopy	retro_ggor_776,
Pan troglodytes	ENSPTRG00000005601	1 retrocopy	retro_ptro_668 ,