RetrogeneDB ID: retro_ptro_428

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:66186997..66187943(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1B10
• Ensembl ID: ENSPTRG00000019718
• Aliases: None
• Description: aldo-keto reductase family 1, member B10 (aldose reductase) [Source:HGNC Symbol;Acc:382]

Sequence

>retro_ptro_428
ATGGCCATCTTTGTGGAGCTCAATACCAAAGCCAAGATGCCCATTGTGGGCCTGGGCACTTGGAAGTCTCCTCTCGGCAA
AGTGAAAGAAGTGGTGAAGGTGGCCATTGATGCAGGATATCGCCACATTGACTGTGCCTATGTCTATCAGAATGAACATG
AGGTGGGGGAAGCCATCCAAGAGAAGATCCAAGAGAAGGCTGTAAAGCGGGAGGACCTCTTCATCATCAACAAGTTGTGG
CCCACTTTCTTTGAGAGACCCCTTGTGAGGAAAGCCTTTGAGAAGACCCTCAAGGATCTGAAGCTGAGTTATCTGGATGT
CTATCTTATTCACTAGCACAGGGATACAAGTCTGGGGATGACTTTTTCCCCAAAGATGATAAAGGTAATATGATCGGTGG
AAAAGCAATGTTCTTGGATGCCTGGGAGGCCATGGAGGAGCTGGTGGATGAGGGGCTGGTGAAAGCCCTTGGGGTCTCCA
ATTTCAACCACTTCCAGATAGAGAGGCTCTTGAACAAACCTGGACTGAAATATAAACCAGTGACTAACCAGGTTGAGTGT
CACCCATACCTCAGGCAGGAGAAACTGATCCAGTACTGCCACTTCAAGGGCATCACCATTATGGCCTACAGCCCCCTAGG
CTCTCTGGATAGACCTTGGGCCAAGCCAGAGGACCCTTCCCTGCTGGAGGATCCCAAGATTAAGGAGATTGCTGCAAGGC
ACGAGAAACCACAGCCCAGGTTCTGATCCATTTCCATATCCAGAGGAATGTGACTGTGATCCCCAAGTCTGTGACACCAG
CACGCATTGTTGAGAACATTCAGGCCTTTGACTTTAAATTGAATGATGAGGAGATGGCAAACATACTCAGCTTCAACAGA
AACTGGAGGGCCCGTAACATGTTGCAATCCTCTCATTTGGAGGACTATCCCTTCGAAGCAGAATAT

Alignment

ORF - retro_ptro_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYQHIDCAYVYQNEHEVGEAIQEKIQEKAVKR
          MA.FVEL.TKAKMPIVGLGTWKSPLGKVKE.VKVAIDAGY.HIDCAYVYQNEHEVGEAIQEKIQEKAVKR
Retrocopy MAIFVELNTKAKMPIVGLGTWKSPLGKVKEVVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKR

Parental  EDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIH-WPQGFKSGDDLFPKDDKGNAIGGKATFL
          EDLFI..KLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIH...QG.KSGDD.FPKDDKGN.IGGKA.FL
Retrocopy EDLFIINKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIH<LAQGYKSGDDFFPKDDKGNMIGGKAMFL

Parental  DAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTA
          DAWEAMEELVDEGLVKALGVSNF.HFQIE.LLNKPGLKYKPVTNQVECHPYL.QEKLIQYCH.KGIT..A
Retrocopy DAWEAMEELVDEGLVKALGVSNFNHFQIERLLNKPGLKYKPVTNQVECHPYLRQEKLIQYCHFKGITIMA

Parental  YSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKK-TTAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFD
          YSPLGS.DRPWAKPEDPSLLEDPKIKEIAA.H.K.TTAQVLI.FHIQRNV.VIPKSVTPARIVENIQ.FD
Retrocopy YSPLGSLDRPWAKPEDPSLLEDPKIKEIAARHEK<TTAQVLIHFHIQRNVTVIPKSVTPARIVENIQAFD

Parental  FKLSDEEMATILSFNRNWRACNVLQSSHLEDYPFDAEY
          FKL.DEEMA.ILSFNRNWRA.N.LQSSHLEDYPF.AEY
Retrocopy FKLNDEEMANILSFNRNWRARNMLQSSHLEDYPFEAEY

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	0.09 RPM
SRP007412_cerebellum	0.00 RPM	0.11 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	3.77 RPM
SRP007412_liver	0.03 RPM	136.04 RPM
SRP007412_testis	0.00 RPM	4.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_428 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_428 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_581
Macaca mulatta	retro_mmul_2455

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019716	6 retrocopies	retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428 ,
Pan troglodytes	ENSPTRG00000019740	1 retrocopy	retro_ptro_217,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,