RetrogeneDB ID: retro_pabe_606

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:67871286..67872232(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1B10
• Ensembl ID: ENSPPYG00000018018
• Aliases: None
• Description: aldo-keto reductase family 1, member B10 (aldose reductase) [Source:HGNC Symbol;Acc:382]

Sequence

>retro_pabe_606
ATGGCCATCTTTGTGGAGCTCAGTACCAAAGCCAAGATGCCCATTGTGGGCCTGGGCACTTGGAAGTCTCCTCTCAGCAA
AGTGAAAGAAGTGGTGAAGGTGGCCATTGATGCAAGATATCGCCACATTGACTGTGCCTATGTCTATCAGAATGAACATG
AGGTGGGGGAAGCCATCCAAGAGAAGATCCAAGAGAAGGCTGTAAAGCGGGAGGACCTCTTCATCATCAACAAGTTGTGG
CCCACTTTCTTTGAGAGACCCCTTGTGAGGAAAGCCTTTGAGAAGACCCTCAAGGATCTGAAGCTGAGTTATCTGGACAT
CTATCTTATTCACTGGCACAGGGATACAAGTCTGGGGATGACTTTTTCCCCAAAGATGATAAAGGTAACATGATCGGTGG
AAAAGCAATGTTCTTGGATGCCCGGGAGGCCATGGAGGAGCTGGTGGACGAGGGGCTGGTGAAAGCCCTTGGGGTCTCCA
CTTTCAACCACTTCCAGATAGAGAGGCTCTTGAACAAACCTGGACTGAAATATAAACCAGTGACTAACCAGGTTGAGTGT
CACCCATACCTCATGCAGGAGAAACTGATCCAGTACTGCCACCCCAAAGGCATCACCATTATGGCCTACAGCCCCCTAGG
CTCTCCGGATAGACCTCGGGCCAAGCCAGAGGACCCTTCCCTGCTGGAGGATCCCAAGATTAAGGAGATTGCTGCAAATC
ACAAAAAACCACAGCCCACGTTCTGATCTGTTTCCATATCCAGAGGAATGTGATTGTGATCCCCAAGTCTGTGACACCAG
CATGCATTGTTGAGAACATTCAGGTCTTTGACTTTAAATTGAATGATGAGGAGATGGCAACCATACTCAGCTTCAACAGA
AACTGGAGGGCCTGCAACATGTTGCAATCCTCTCATTCGGAGGACTATCCCTTCAGTGCAGAATAT

Alignment

ORF - retro_pabe_606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVTVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKR
          MA.FVELSTKAKMPIVGLGTWKSPL.KVKE.V.VAIDA.YRHIDCAYVYQNEHEVGEAIQEKIQEKAVKR
Retrocopy MAIFVELSTKAKMPIVGLGTWKSPLSKVKEVVKVAIDARYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKR

Parental  EDLFIVSKVWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHW-PQGFKSGDDLFPKDDKGNAIGGKATFL
          EDLFI..K.WPTFFERPLVRKAFEKTLKDLKLSYLD.YLIHW..QG.KSGDD.FPKDDKGN.IGGKA.FL
Retrocopy EDLFIINKLWPTFFERPLVRKAFEKTLKDLKLSYLDIYLIHW<AQGYKSGDDFFPKDDKGNMIGGKAMFL

Parental  DAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTA
          DA.EAMEELVDEGLVKALGVS.F.HFQIE.LLNKPGLKYKPVTNQVECHPYL.QEKLIQYCH.KGIT..A
Retrocopy DAREAMEELVDEGLVKALGVSTFNHFQIERLLNKPGLKYKPVTNQVECHPYLMQEKLIQYCHPKGITIMA

Parental  YSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHK-KTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFD
          YSPLGSPDRP.AKPEDPSLLEDPKIKEIAA.HK.KT.A.VLI.FHIQRNVIVIPKSVTPA.IVENIQVFD
Retrocopy YSPLGSPDRPRAKPEDPSLLEDPKIKEIAANHK<KTTAHVLICFHIQRNVIVIPKSVTPACIVENIQVFD

Parental  FKLSDEEMATILSFNRNWRACNVLQSSHLEDYPFDAEY
          FKL.DEEMATILSFNRNWRACN.LQSSH.EDYPF.AEY
Retrocopy FKLNDEEMATILSFNRNWRACNMLQSSHSEDYPFSAEY

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.15 RPM
SRP007412_kidney	0.00 RPM	0.89 RPM
SRP007412_liver	0.00 RPM	8.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_606 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_606 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_606 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 28 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	ENSPPYG00000018017	8 retrocopies	retro_pabe_1050, retro_pabe_1089, retro_pabe_1176, retro_pabe_1672, retro_pabe_2411, retro_pabe_3691, retro_pabe_370, retro_pabe_694,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606 ,
Pongo abelii	ENSPPYG00000018037	1 retrocopy	retro_pabe_406,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,