RetrogeneDB ID: retro_ptro_2374

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:101445378..101446153(+)
• Located in intron of: ENSPTRG00000018448

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D1
• Ensembl ID: ENSPTRG00000015661
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 1 [Source:UniProtKB/TrEMBL;Acc:K7AGK0]

Sequence

>retro_ptro_2374
AACAAGTTGAAATCATCGCAGAAGGATAAAGTTTGTCAGTTTATGATCTTCACACAATCTAGTGAAAAAAACCGCAGTAA
GTTGTCTATCTCAAAATGACTGGAAGTTAGATGTTGCAACAGATAATTTTTTCCAAAATCCTGAACTTTATATACGAGAG
AGTGTAAAAGGATCACTGGAAAGGAAGAAGTTAGAACAACTGTACAATAGAGACAAAGATCCTCAAAATGAGAATAAAAT
TGGAATAGATGGTATATAGCAGTTCTGTGATGGCCTGGCACTCAATCCAGCCATCATTAGTGTGTTGATTATTGCATGGA
TGTTCAGAGCAGCAATACAGTGTGAGTTCTCCAAACAGGAGTTCATGGATGGCATGACAGAATTAGGATGTGACAGCATA
GAAAAACTAAAGGCCCAGATACCCAAGATGTAACAAGAATTGCAAGAACCAGGACAATTTAAGGATTTTTACCAGTTTAC
TTTTAATTTTGCAAAGAATCCAAGACAAAAAGGATTAGATCTAGAAATGGCCATTGCCTACTGGAACTTAGTGCTTAATA
GAAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTTGGAACATCACAAACAATCAATACCAAAAGACACTTGGAAT
CTTCTTTTAGACTTCAGTACAGTGATTGCAAATCACGTGTCTAATTATGATGAAGAAGGAGCATGGCCTGTTCTTATTGA
TGACTTTGTGGAATTTGCACGCCCTCAAACTGCTGGGACAAAAAGTACAACAGTG

Alignment

ORF - retro_ptro_2374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSE-KTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYN
          NKLKSSQKDKV.QFMIFTQSSE.KTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSL.RKKLEQLYN
Retrocopy NKLKSSQKDKVCQFMIFTQSSE>KTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLERKKLEQLYN

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQ
          R.KDPQ.ENKIGIDGI.QFCD.LAL.PA.ISVLIIAW.FRAA.QCEFSKQEFMDGMTELGCDSIEKLKAQ
Retrocopy RDKDPQNENKIGIDGI*QFCDGLALNPAIISVLIIAWMFRAAIQCEFSKQEFMDGMTELGCDSIEKLKAQ

Parental  IPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK
          IPKM.QEL.EPG.FKDFYQFTFNFAKNP.QKGLDLEMAIAYWNLVLN.RFKFLDLWNKFLLEHHK.SIPK
Retrocopy IPKM*QELQEPGQFKDFYQFTFNFAKNPRQKGLDLEMAIAYWNLVLNRRFKFLDLWNKFLLEHHKQSIPK

Parental  DTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
          DTWNLLLDFST.IA...SNYDEEGAWPVLIDDFVEFARPQ.AGTKSTTV
Retrocopy DTWNLLLDFSTVIANHVSNYDEEGAWPVLIDDFVEFARPQTAGTKSTTV

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	0.21 RPM	15.82 RPM
SRP007412_cerebellum	0.82 RPM	11.94 RPM
SRP007412_heart	0.44 RPM	9.88 RPM
SRP007412_kidney	0.42 RPM	15.30 RPM
SRP007412_liver	0.43 RPM	7.30 RPM
SRP007412_testis	2.21 RPM	249.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2374 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2374 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3502
Gorilla gorilla	retro_ggor_2368
Pongo abelii	retro_pabe_2894
Macaca mulatta	retro_mmul_1782

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232, retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374 ,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,