RetrogeneDB ID: retro_pabe_2714

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:2645689..2646712(-)
• 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_2714
GCAGGAGTCATAACACTAAACAGACCAAAGTTCCTAAATGCACTGACTCTTAATATGATTTGGCAGATTTATCCACAGCT
AGAGAAGTGGGAACAAGATCCTGAAACTCTCCTGATCATTATAAAGAGAGTCAGAGGAAAGACTTTCTGTGCTGGGAGTG
ATATTAGAGTGATCACAGAAGCTGAAAAGGCAAAACAGAAGATAGCGCCAGTTTTCTTCAGAAAGGAATATATGCTGAAC
AATGCTTTTGGTTCTTGCCAGAAACCTTATGTTGCACTTATTCATGGAATTACAGTGGGTGGGGGAGTTGGTCTGTCAGT
TCACGGACAGCTTCAAGTGGCTACAGAAAAGTATCTTTTTGCCATGCCAGAAACGGCAGTAAGACTGTTCCCTGATGTGG
ATGGAGGTTATTTCTTGCCACGACTTCAAGGGAAACTTGGTTACTTCCTTGCATTAACAGGATTCAGACTAAAATGAAAA
GATGTGTACAGAGCAGGAATTGCTACACACTTTGTAGATTCTGAAAAGTTGGGCATGTTAGAGGAAGATTTGTTAGCCTT
GAAATCTCCTTCAAAAGAAAATATTGCAGCTGTCTTAGAAAATTACCATATGGAGTCTAAGATTGATGAAGAGAAGTCTT
TTATACTTGAGGAACACATGGGCAAAATAAACAGTTGCTTTTCAGCCAATACTGTGGGACAAATTATTGAAAACTTACAG
CAAGATGGTTCATCTTTTGCCCTAAAGCAATTGAAGGTAATTAATAACATGTCTCCAACATCTCTAAAGATCACACTAAG
GTAACTCCTGGAAGGGTCTTGAAAGACCTTGCAAGAAGTACTAACTATGGAGTATCAGCTAAGTCAAGCTTGTATGGGGA
GTCATGACTTTTATGAAGGCGTCAGAGCTGTTTTAATTAATAAAGACCAGAGTCCAAAATGGAAACTAGCTGATCTAAAA
GAAGTTACTGATGAAGATTTGAATAATCACTTTAAGTCTTTGGGAAGCAATGGTTTGAAATTT

Alignment

ORF - retro_pabe_2714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 88.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

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  DKSFILEEHMDKINSCFSANTVEEIIENLQQDGSSFALEQLKVINKMSPTSLKITLRQLMEGSSKTLQEV
          .KSFILEEHM.KINSCFSANTV..IIENLQQDGSSFAL.QLKVIN.MSPTSLKITLR.L.EGS.KTLQEV
Retrocopy EKSFILEEHMGKINSCFSANTVGQIIENLQQDGSSFALKQLKVINNMSPTSLKITLR*LLEGS*KTLQEV

Parental  LTMEYRLSQACMRGHDFHEGVRAVLIDKDQSPKWKPADLKEVTEEDLNNHFKSLGSSDLKF
          LTMEY.LSQACM..HDF.EGVRAVLI.KDQSPKWK.ADLKEVT.EDLNNHFKSLGS..LKF
Retrocopy LTMEYQLSQACMGSHDFYEGVRAVLINKDQSPKWKLADLKEVTDEDLNNHFKSLGSNGLKF

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_2714 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2714 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2714 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3285
Pan troglodytes	retro_ptro_2222
Gorilla gorilla	retro_ggor_1317
Macaca mulatta	retro_mmul_2062

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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,