RetrogeneDB ID: retro_pabe_2827

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5_random:17541114..17541967(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBCH
• Ensembl ID: ENSPPYG00000013021
• Aliases: None
• Description: 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial [Source:RefSeq peptide;Acc:NP_001127380]

Sequence

>retro_pabe_2827
GCAGGAGTCATAACACTAAACAGACCAAAGTTCCTAAATGCACTGACTCTTAATATGATTTGGCAGATTTATCCACAGCT
AGAGAAGTGGGAACAAGATCCTGAAACTCTCCTGATCATTATAAAGAGAGTCAGAGGAAAGACTTTCTGTGCTGGGAGTG
ATATTAGAGTGATCACAGAAGCTGAAAAGGCAAAACAGAAGATAGCGCCAGTTTTCTTCAGAAAGGAATATATGCTGAAC
AATGCTTTTGGTTCTTGCCAGAAACCTTATGTTGCACTTATTCATGGAATTACAGTGGGTGGGGGAGTTGGTCTGTCAGT
TCACGGACAGCTTCAAGTGGCTACAGAAAAGTATCTTTTTGCCATGCCAGAAACGGCAGTAAGACTGTTCCCTGATGTGG
ATGGAGGTTATTTCTTGCCACGACTTCAAGGGAAACTTGGTTACTTCCTTGCATTAACAGGATTCAGACTAAAATGAAAA
GATGTGTACAGAGCAGGAATTGCTACACACTTTGTAGATTCTGAAAAGTTGGGCATGTTAGAGGAAGATTTGTTAGCCTT
GAAATCTCCTTCAAAAGAAAATATTGCAGCTGTCTTAGAAAATTACCATATGGAGTCTAAGATTGATGAAGAGAAGTCTT
TTATACTTGAGGAACACATGGGCAAAATAAACAGTTGCTTTTCAGCCAATACTGTGGGACAAATTATTGAAACTTACAGC
AAGATGGTTCATCTTTTGCCCTAAAGCAATTGAAGGAATTAATAACATGTCTCCAACATCTCTAAAGATCACACTAAGTA
ACTCCTGAAGGTCTTGAAAGACCTTGCAGAGTACTAACTATGAGTATCAGCTA

Alignment

ORF - retro_pabe_2827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.74 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGVITLNRPKFLNALTLNMIQKIYPQLKKWEQDPETFLIIIKGAGGKAFCAGGDIRVISEAEKAKQKIAP
          AGVITLNRPKFLNALTLNMI..IYPQL.KWEQDPET.LIIIK...GK.FCAG.DIRVI.EAEKAKQKIAP
Retrocopy AGVITLNRPKFLNALTLNMIWQIYPQLEKWEQDPETLLIIIKRVRGKTFCAGSDIRVITEAEKAKQKIAP

Parental  VFFREEYMLNNAVGSCQKPYVALIHGITMGGGVGLSVHGQFRVATEKCLFAMPETAIGLFPDVGGGYFLP
          VFFR.EYMLNNA.GSCQKPYVALIHGIT.GGGVGLSVHGQ..VATEK.LFAMPETA..LFPDV.GGYFLP
Retrocopy VFFRKEYMLNNAFGSCQKPYVALIHGITVGGGVGLSVHGQLQVATEKYLFAMPETAVRLFPDVDGGYFLP

Parental  RLQGKLGYFLALTGFRLKGRDVYRAGIATHFVDSEKLAMLEEDLLALKSPSKENIASVLENYHTESKIDR
          RLQGKLGYFLALTGFRLK..DVYRAGIATHFVDSEKL.MLEEDLLALKSPSKENIA.VLENYH.ESKID.
Retrocopy RLQGKLGYFLALTGFRLK*KDVYRAGIATHFVDSEKLGMLEEDLLALKSPSKENIAAVLENYHMESKIDE

Parental  DKSFILEEHMDKINSCFSANTVEEIIE-NLQQDGSSFALEQLKV-INKMSPTSLKITLRQLMEGSSKTLQ
          .KSFILEEHM.KINSCFSANTV..IIE.NLQQDGSSFAL.QLK..IN.MSPTSLKITL......S.KTLQ
Retrocopy EKSFILEEHMGKINSCFSANTVGQIIE<NLQQDGSSFALKQLKE<INNMSPTSLKITLSNS*R-S*KTLQ

Parental  EVLTMEYRL
          .....EY.L
Retrocopy ST-NYEYQL

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	10.73 RPM
SRP007412_cerebellum	0.00 RPM	16.29 RPM
SRP007412_heart	0.00 RPM	12.01 RPM
SRP007412_kidney	0.00 RPM	69.51 RPM
SRP007412_liver	0.00 RPM	31.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2827 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000003341	1 retrocopy	retro_fcat_890,
Homo sapiens	ENSG00000198130	1 retrocopy	retro_hsap_3285,
Gorilla gorilla	ENSGGOG00000004988	1 retrocopy	retro_ggor_1317,
Macaca mulatta	ENSMMUG00000007283	1 retrocopy	retro_mmul_2062,
Mus musculus	ENSMUSG00000041426	1 retrocopy	retro_mmus_294,
Nomascus leucogenys	ENSNLEG00000006646	1 retrocopy	retro_nleu_1351,
Pongo abelii	ENSPPYG00000013021	2 retrocopies	retro_pabe_2714, retro_pabe_2827 ,
Pan troglodytes	ENSPTRG00000012741	1 retrocopy	retro_ptro_2222,
Tupaia belangeri	ENSTBEG00000004132	1 retrocopy	retro_tbel_3398,