RetrogeneDB ID: retro_ggor_2316

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:16748425..16749103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH1
• Ensembl ID: ENSGGOG00000007085
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G3QVZ2]

Sequence

>retro_ggor_2316
AGAGAGGAAAGATTTACTGAAAATGTAAAAGTCATCAAATGGCAGGGTGCAGCCTTGGAGAAATATGACAAGAAGTTCGT
TAAGGTTATTGTTATGGGAAACCCAGCCAATATCAACTGCCTGACTGCCTCCAAGTTGGCTCCATCCATCTTCAATGAGA
ACTTCAGTTGCTTGACTTGTTTGGATCACAACCAAACTCAAGTTCGAATTACTCTTAAACTTGGTGTGACTGCTGACAAT
GTAAAGAATATTACATATCTGGGGAAACCATTCCTTCACTCAGTATCCAGATGTCAACCAAGCCAAGGTGAAATTGCAAG
GAAAGGAAGTTGTTTATGAAGCTCTGAAACATGACAGCTGGCCCCAGGGAGAATTCATGGCTGTGCAGCAACATGGTGCT
GCTGTCATCGAGGCTCAAAAACCATCCAGGGCAACGTCCACTACGAGAGCCATCTCCAACCACCTCAGAGACATCTGGCT
TGGAACCCCATAGGGAGAGTCTGTGTCCAGTGGGGTTATCTCTAATAGTAACTCCTATGGTATTCCCAGTCATTGTTCTA
CTCATTCTCTGTTGTATTCAAGAATAAGACCTGGAAATTTGCTGAAGCTCTCTCCATTAATGATTCCTCATGTAAGAAGA
TGGATCTTACTGCAAAGGAACTGGCAGGGAAGAAAAAG

Alignment

ORF - retro_ggor_2316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.83 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQV
          R......NVK..K.QGAAL.KY.KK.VKVIV.GNPAN.NCLTASK.APSI..ENFSCLT.LDHN......
Retrocopy REERFTENVKVIKWQGAALEKYDKKFVKVIVMGNPANINCLTASKLAPSIFNENFSCLTCLDHNQTQVRI

Parental  ALKLGVTANDVKNVI-IWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIK
          .LKLGVTA..VKN...IWGNHS.TQYPDVN.AKVKLQGKEV.VYEALK.DSW..GEF...VQQ.GAAVI.
Retrocopy TLKLGVTADNVKNIT>IWGNHSFTQYPDVNQAKVKLQGKEV-VYEALKHDSWPQGEFM-AVQQHGAAVIE

Parental  ARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYGVP-DDLLYSFPVVIKNKTWKFVEGLPI
          A.K.S.A.S...AI..H.RDIW.GTP.GE.VS.GVIS..NSYG.P...L.YSF.VV.KNKTWKF.E.L.I
Retrocopy AQKPSRATSTTRAISNHLRDIWLGTP*GESVSSGVISNSNSYGIP<QSLFYSFSVVFKNKTWKFAEALSI

Parental  NDFSREKMDLTAKELTEEKE
          ND.S..KMDLTAKEL...K.
Retrocopy NDSSCKKMDLTAKELAGKKK

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	290.46 RPM
SRP007412_cerebellum	0.00 RPM	96.01 RPM
SRP007412_heart	0.00 RPM	143.90 RPM
SRP007412_kidney	0.00 RPM	199.58 RPM
SRP007412_liver	0.00 RPM	75.28 RPM
SRP007412_testis	0.00 RPM	46.93 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_2316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2316 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3426
Pan troglodytes	retro_ptro_2326
Pongo abelii	retro_pabe_2839
Macaca mulatta	retro_mmul_1750

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848, retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316 ,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,