RetrogeneDB ID: retro_ggor_2368

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:100366608..100367383(+)
• Located in intron of: ENSGGOG00000002790

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D1
• Ensembl ID: ENSGGOG00000010767
• Aliases: None
• Description: None

Sequence

>retro_ggor_2368
AACAAGTTGAAATCATCGCAGAAGGATAAAGTTTGTCAGTTTATGATCTTCACACAATTTAGTGAAAAAAACCGCAGTAA
GTTGTCTATCTCAAAATGACTGGAAGTTAGATGTTGCAACAGATAATTTTTTCCAAAATCCTGAACTTTATATATGAGAG
AGTGTAAAAGGATCACTGGAAAGGAAGAAGTTAGAACAACTGTACAATAGAGACAAAGATCCTCAAAATGAGAATAAAAT
TGGAATAGATGGTATATAGCAGTTCTGTGATGGCCTGGCACTCAATCCAGCCAGCATTAGTGTGTTGATTATTGCATGGA
TGTTCAGAGCAGCAATACAGTGTGAGTTCTCCAAAAAGGAGTTCATGGATGGCATGACAGAATTAGGATGTGACAGCATA
GAAAAACTAAAGGCCCAGATACCCAAGATGTAACAAGAATCGAAAGAACCAGGACAATTTAAGGATTTTTACCAGTTAAC
TTTTAATTTTGCAAAGAATCCAAGACAAAAAGGATTAGATCTAGAAATGGCCATTGCCTACTGGAACTTAGTGCTTAATA
GAAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTTGGAACATCACAAACAATCAATACCAAAAGACACTTGGAAT
CTTCTTTTAGACTTCAGTACAGTGATTGCAAATCACGTGTCTAATTATGATGAAGAAGGAGCATGGCCTGTTCTTATTGA
TGACTTTGTGGAATTTGCACGCCCTCAAACTGCTGGGACAAAAAGTACAACAGTG

Alignment

ORF - retro_ggor_2368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSE-KTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYN
          NKLKSSQKDKV.QFMIFTQ.SE.KTAVSCLSQNDWKLDVATDNFFQNPELYI.ESVKGSL.RKKLEQLYN
Retrocopy NKLKSSQKDKVCQFMIFTQFSE>KTAVSCLSQNDWKLDVATDNFFQNPELYI*ESVKGSLERKKLEQLYN

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQ
          R.KDPQ.ENKIGIDGI.QFCD.LAL.PASISVLIIAW.FRAA.QCEFSK.EFMDGMTELGCDSIEKLKAQ
Retrocopy RDKDPQNENKIGIDGI*QFCDGLALNPASISVLIIAWMFRAAIQCEFSKKEFMDGMTELGCDSIEKLKAQ

Parental  IPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK
          IPKM.QE.KEPG.FKDFYQ.TFNFAKNP.QKGLDLEMAIAYWNLVLN.RFKFLDLWNKFLLEHHK.SIPK
Retrocopy IPKM*QESKEPGQFKDFYQLTFNFAKNPRQKGLDLEMAIAYWNLVLNRRFKFLDLWNKFLLEHHKQSIPK

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	0.96 RPM	11.80 RPM
SRP007412_cerebellum	0.67 RPM	10.40 RPM
SRP007412_heart	0.06 RPM	1.59 RPM
SRP007412_kidney	0.16 RPM	15.74 RPM
SRP007412_liver	0.34 RPM	13.27 RPM
SRP007412_testis	2.59 RPM	148.15 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2368 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3502
Pan troglodytes	retro_ptro_2374
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,