RetrogeneDB ID: retro_pabe_2839

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:16708746..16709424(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH1
• Ensembl ID: ENSPPYG00000012373
• Aliases: None
• Description: malate dehydrogenase 1, NAD (soluble) [Source:HGNC Symbol;Acc:6970]

Sequence

>retro_pabe_2839
AGAGAGGAAAGATTTACTGAAAATGTAAAAATCTTCAAATGGCAGGGTGCAGCCTTGGAGAAATATGACAAGAAGTTCGT
TAAGGTTATTGTTATGGGAAACCCAGCCAATATCAACTGCCTGACTGCCTCCAAGTTGGCTCCATCCATCTTCAACGAGA
ACTTCAGTTGCTTGACTTGTTTGGATCACAACCAAACTCAAGTTTAAATTACTCTTAAACTTGGTGTGACTGCTGACAAT
GTAAAGAATATTACATATCTGGGGAAACCATTCCTTGACTCAGTATCCAGATGTCAACCAAGCCAAGGTGAAATTGCAAG
GAAAGGAAGTTGTTTATGAAGCTCTGAAACATGACAGCTGGCCCCAGGGAGAATTCACAGCTGTGCAGCAACACGGTGCT
GCTGTCATCAAGGCTCTAAAACCATCCAGGGCAATGTTCACTACAAGAGCCATCTCCAACCACCTCAGAGACATCTGGCT
TGGAACCCCATAGGGAGAGTCTGTGTCCACTGGGGTTATCTCTGATAGTGACTCCTATGGTATTCCCAGTAATCGTTCTA
CTCGTTCTCTGTTGTGTTCAAGAATAAGACCTGGAAATTTGTTGAAGCTGTCTCCATTAATGATTCCTCATGTAAGAAGA
TGGATCTTACTGCAAAGGAACTGGCAGGGAAGAAAAAG

Alignment

ORF - retro_pabe_2839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 68.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQI
          R......NVKIFK.QGAAL.KY.KK.VKVIV.GNPAN.NCLTASK.APSI..ENFSCLT.LDHN.....I
Retrocopy REERFTENVKIFKWQGAALEKYDKKFVKVIVMGNPANINCLTASKLAPSIFNENFSCLTCLDHNQTQV*I

Parental  ALKLGVTANDVKNVI-IWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIK
          .LKLGVTA..VKN...IWGNHS.TQYPDVN.AKVKLQGKEV.VYEALK.DSW..GEF.T.VQQ.GAAVIK
Retrocopy TLKLGVTADNVKNIT>IWGNHSLTQYPDVNQAKVKLQGKEV-VYEALKHDSWPQGEF-TAVQQHGAAVIK

Parental  ARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYGVPDD-LLYSFPVVIKNKTWKFVEGLPI
          A.K.S.AM....AI..H.RDIW.GTP.GE.VS.GVISD..SYG.P.....YSF.VV.KNKTWKFVE...I
Retrocopy ALKPSRAMFTTRAISNHLRDIWLGTP*GESVSTGVISDSDSYGIPSN<SFYSFSVVFKNKTWKFVEAVSI

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	234.87 RPM
SRP007412_cerebellum	0.00 RPM	163.92 RPM
SRP007412_heart	0.00 RPM	342.01 RPM
SRP007412_kidney	0.00 RPM	109.85 RPM
SRP007412_liver	0.00 RPM	62.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2839 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2839 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3426
Pan troglodytes	retro_ptro_2326
Gorilla gorilla	retro_ggor_2316
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,