RetrogeneDB ID: retro_ptro_2222

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:2815879..2816838(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBCH
• Ensembl ID: ENSPTRG00000012741
• Aliases: None
• Description: None

Sequence

>retro_ptro_2222
CAGATGTATCCATGGCTAGAGAAGTGGGAAGAAGATCCTGAAACTCTCCTGATCATTATAAAGGGAGCCGGAGGAAAGGC
TTTCTGTGATGGGAGTGATATTAGAGTCATTTCGGAGGCTGAAAAGGCAAAACGGAAGATAGCGCCAGTTTTCTTCAGAG
AAGAATATATGCTGAACAATGCTTTTGGTTCTTGCCAGAAACCTTATGTTGCACTTATTCATGGAATTACAATGGGTGGG
AGAGTTGGTCGTCAGTCCATGGGCAGCTTCAAGTGGCTACAGAAAAGTGTCTTTTTGCCATGCCAGAAACCGCAGTAGGA
CTGTTCCCTGATGGGGGTGGAGGTTATTTCTTGCCATGACTTCAAGGAAAACTTGGTTACATCCTTTCATTAACAGGATT
CAGACTAAAATGAAAAGATGTGTACAGAGCAGGAATTGCTACACACTTTGTAGATTCTGAAAAGTTGGGCATGTTAGAGG
AAGATTTGTTAGCCTTGAAATCTCCTTCAAAAGAAAATATTGCAGCTGTCTTAGAAAATTACCATATGGAGTCTAAGATT
GATGAAGACAAGTCTTTTATACTTGAGGAACACATGGGCAAAATAAACAGTTGCTTTTCAGCCAATACTGTGGGACAAAT
TATTGAAAACTTACAGCAAGATTGTTCATCTTTTGCCCTAGAGCAATTGAAGGTAATTAATAACATGTCTCCAACATCTC
TAAAGATCACACTAAGGTAACTCCTGGAGGGGTCTTGAAAGACCTTGCAAGAAGTACTAACTATGGAGTATCAGCTAAGT
CAAGCTTGTATGGAGGGTCATGACTTTTATGAAGGTGTCAGAGCTGTTTTAATTAATAAAGACCAGAATCCAAAATGGAA
ACCAGCTGATCTAAAAGAAGTTACTGATGAAGATTTGAATAATCACATTAAGTCTTTGGGAAGCAATGATTTGAAATTT

Alignment

ORF - retro_ptro_2222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.23 %
• Parental protein coverage: 82.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIYPQLKKWEQDPETFLIIIKGAGGKAFCAGGDIRVISEAEKAKQKIAPVFFREEYMLNNAVGSCQKPYV
          Q.YP.L.KWE.DPET.LIIIKGAGGKAFC.G.DIRVISEAEKAK.KIAPVFFREEYMLNNA.GSCQKPYV
Retrocopy QMYPWLEKWEEDPETLLIIIKGAGGKAFCDGSDIRVISEAEKAKRKIAPVFFREEYMLNNAFGSCQKPYV

Parental  ALIHGITMGGGVGL-SVHGQFRVATEKCLFAMPETAIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGR
          ALIHGITMGG.VG..SVHGQ..VATEKCLFAMPETA.GLFPD.GGGYFLP.LQGKLGY.L.LTGFRLK..
Retrocopy ALIHGITMGGRVGR<SVHGQLQVATEKCLFAMPETAVGLFPDGGGGYFLP*LQGKLGYILSLTGFRLK*K

Parental  DVYRAGIATHFVDSEKLAMLEEDLLALKSPSKENIASVLENYHTESKIDRDKSFILEEHMDKINSCFSAN
          DVYRAGIATHFVDSEKL.MLEEDLLALKSPSKENIA.VLENYH.ESKID.DKSFILEEHM.KINSCFSAN
Retrocopy DVYRAGIATHFVDSEKLGMLEEDLLALKSPSKENIAAVLENYHMESKIDEDKSFILEEHMGKINSCFSAN

Parental  TVEEIIENLQQDGSSFALEQLKVINKMSPTSLKITLRQLMEGSSKTLQEVLTMEYRLSQACMRGHDFHEG
          TV..IIENLQQD.SSFALEQLKVIN.MSPTSLKITLR.L.EGS.KTLQEVLTMEY.LSQACM.GHDF.EG
Retrocopy TVGQIIENLQQDCSSFALEQLKVINNMSPTSLKITLR*LLEGS*KTLQEVLTMEYQLSQACMEGHDFYEG

Parental  VRAVLIDKDQSPKWKPADLKEVTEEDLNNHFKSLGSSDLKF
          VRAVLI.KDQ.PKWKPADLKEVT.EDLNNH.KSLGS.DLKF
Retrocopy VRAVLINKDQNPKWKPADLKEVTDEDLNNHIKSLGSNDLKF

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	6.79 RPM
SRP007412_cerebellum	0.00 RPM	8.25 RPM
SRP007412_heart	0.03 RPM	19.79 RPM
SRP007412_kidney	0.00 RPM	52.67 RPM
SRP007412_liver	0.00 RPM	17.25 RPM
SRP007412_testis	0.00 RPM	29.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2222 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2222 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3285
Gorilla gorilla	retro_ggor_1317
Pongo abelii	retro_pabe_2714
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,