RetrogeneDB ID: retro_ggor_3043

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:89057830..89058525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSGGOG00000001932
• Aliases: None
• Description: None

Sequence

>retro_ggor_3043
AAAGTGACGGGCAGTCTGGAAACCAAGTACAGATGGACTGAGTACGGCCTGATGTTTACAGAGAAATAGAACACCGACAA
TACACTAGGCACCGAGATTACTGTGGAAGATCAGCTTGCACGTGGACTGAAGCTGACCTTCGATTCATCCTTCTTACCTA
AGACTAGGGGAAAAAAGATGCTAAAATCAAGACAGGTTAGAAGCAGGAGCACATTACCCTGGACTACGACATAGATTTCG
ACATTGCTGGGCCTTCCATCCGGGCTGCTCTGGTGCTGGGTTACAAGGGCTGGCTGGCCGGCTACCAGATGAATTTTGAG
ACTGCAAAGTCCGGAGTGACCCAGAGCAACTTTGCAGTTGGCTACAAGACTGATGAATTCCAACTTCACACTAATGTGAA
TGATGGGACAGAGTTTGGCGGCCTCATTTACCAGAAAGTGAACAAGAAGTTGGAGACTGCTGTCAATCTCACCTGGACAG
CAGGAAACAGTAACACGCGTTTCAAAATAGCAGCCAAGTATTTGATTGACCCTGAAGCCTGCTTCTTGGCTAAAGTGAAC
AACTCCAGCCTGATAGGTTTAGGATACACTCAGACCCTAAAGCCAGGTATCAAACTGACACTGTCAGCTCTTCTGGATGG
CAAGAACGTCAATGCTGGTGGCCACAAGCTTGGTCTAGGACTGGAATTTCAAGCA

Alignment

ORF - retro_ggor_3043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.66 %
• Parental protein coverage: 81.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KASGNLETKYKVCNYGLTFTQKWNTDNTLGTEISWENKLAEGLKLTLDTIFVPNT-GK-KSGKLKASYKR
          K..G.LETKY....YGL.FT.K.NTDNTLGTEI..E..LA.GLKLT.D..F.P.T.GK.K..K.K...K.
Retrocopy KVTGSLETKYRWTEYGLMFTEK*NTDNTLGTEITVEDQLARGLKLTFDSSFLPKTRGK<KDAKIKTG*KQ

Parental  DCFSVGSNVDIDFSGPTIYGWAVLAFEGWLAGYQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEF
          .........D.D..GP.I....VL...GWLAGYQM.F.TAKS...Q.NFA.GYK...FQLHT.VNDGTEF
Retrocopy EHITLDYDIDFDIAGPSIRAALVLGYKGWLAGYQMNFETAKSGVTQSNFAVGYKTDEFQLHTNVNDGTEF

Parental  GGSIYQKVNEKIETSINLAWTAGSNNTRFGIAAKYMLDCRTSLSAKVNNASLIGLGYTQTLRPGVKLTLS
          GG.IYQKVN.K.ET..NL.WTAG..NTRF.IAAKY..D......AKVNN.SLIGLGYTQTL.PG.KLTLS
Retrocopy GGLIYQKVNKKLETAVNLTWTAGNSNTRFKIAAKYLIDPEACFLAKVNNSSLIGLGYTQTLKPGIKLTLS

Parental  ALIDGKNFSAGGHKVGLGFELEA
          AL.DGKN..AGGHK.GLG.E..A
Retrocopy ALLDGKNVNAGGHKLGLGLEFQA

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	1.82 RPM	121.04 RPM
SRP007412_cerebellum	0.67 RPM	98.46 RPM
SRP007412_heart	0.81 RPM	64.63 RPM
SRP007412_kidney	1.59 RPM	66.57 RPM
SRP007412_liver	0.34 RPM	47.19 RPM
SRP007412_testis	0.93 RPM	121.94 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_3043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3043 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4872
Homo sapiens	retro_hsap_4930
Macaca mulatta	retro_mmul_2613

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005095	1 retrocopy	retro_amel_729,
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Canis familiaris	ENSCAFG00000005502	5 retrocopies	retro_cfam_1513, retro_cfam_2146, retro_cfam_258, retro_cfam_665, retro_cfam_713,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Dasypus novemcinctus	ENSDNOG00000013885	1 retrocopy	retro_dnov_1753,
Equus caballus	ENSECAG00000000438	1 retrocopy	retro_ecab_799,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Homo sapiens	ENSG00000078668	1 retrocopy	retro_hsap_1375,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043 ,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Gorilla gorilla	ENSGGOG00000010880	3 retrocopies	retro_ggor_693, retro_ggor_875, retro_ggor_981,
Microcebus murinus	ENSMICG00000010235	1 retrocopy	retro_mmur_1361,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Otolemur garnettii	ENSOGAG00000016163	4 retrocopies	retro_ogar_2770, retro_ogar_2870, retro_ogar_589, retro_ogar_995,
Pongo abelii	ENSPPYG00000018554	8 retrocopies	retro_pabe_1145, retro_pabe_1960, retro_pabe_2304, retro_pabe_3163, retro_pabe_3665, retro_pabe_3791, retro_pabe_819, retro_pabe_971,
Pan troglodytes	ENSPTRG00000020205	2 retrocopies	retro_ptro_2548, retro_ptro_945,
Pteropus vampyrus	ENSPVAG00000014822	2 retrocopies	retro_pvam_637, retro_pvam_907,
Rattus norvegicus	ENSRNOG00000019277	1 retrocopy	retro_rnor_1596,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000007112	1 retrocopy	retro_tsyr_918,