RetrogeneDB ID: retro_pabe_406

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:83685959..83686707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AKR1D1
• Ensembl ID: ENSPPYG00000018037
• Aliases: None
• Description: aldo-keto reductase family 1, member D1 [Source:HGNC Symbol;Acc:388]

Sequence

>retro_pabe_406
GTGAAGGTTGTCATTGGTCTGGGGTGCTGACACACTGATGAAGCCTACATATACCAGAATGAAGACACAGCTGGGGAGGC
CATCAGGGGGGAAATAGCAGAAGGAAAGGTGCAGAGGAAGGATATCTTCTACTGTGGAAAACTGTGGGCTACAAATCACG
ACCCAGAGCTGGTCTGCCCAAGCCTAGAGAGGATGCTCAAGGTCCTCCAGCTAGATTGTGTGGATCTTTACATCATTGAA
ATATCCATGGCCCCTAAGCCAGAAGATGAAATCTACCCTATAGGTGAGAATGGCAAATGGTTATATCATAAGTCAAATCT
GTGTGCCACTTGGGAGACTTCGGAAGCTTGTAAAGATGCTGGCTTGGTGAAATCCCTCGGAGTATCCAGTTTTAATAGCA
GGCCAGCTGGAACTCATCCAGAACAACCCAGGACTCAAATCCAAGCCAGTCAGCAATGAGGTTGAGTGCCACCCATATTA
CACCCAGCCAAAACTTTTGAAATTTTGCCAACAACATGACATTGTCATGATTGCATATAGCCCTTTGGGGACCACTAGGA
ATCCAACCTGGACAAATATGTCTTCTCCACCTTCGTTAAAAGATGCACTTCTAAAAAGGTGCAATAAGATCACAGCTCAA
GTTATTTTGCATTTCAACATCCACCAAGGGGTGGTTATCATTCCTAAAAGCTTTAATCCTGAAAAGATCAAGGAAAACCT
TCAGGCCTTTGACTTTTCTCTCACTGAA

Alignment

ORF - retro_pabe_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.59 %
• Parental protein coverage: 77.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKVAIDTGYRHIDGAYIYQNEHEVGEAIREKIAEGKVRREDIFYCGXLWATNHVPEMVRPTLERTLRVLQ
          VKV.I..G..H.D.AYIYQNE...GEAIR..IAEGKV.R.DIFYCG.LWATNH.PE.V.P.LER.L.VLQ
Retrocopy VKVVIGLGC*HTDEAYIYQNEDTAGEAIRGEIAEGKVQRKDIFYCGKLWATNHDPELVCPSLERMLKVLQ

Parental  LDYVDLYIIEVPMAFKPGDEIYPRDENGKWLYHKSNLCATWEAMEACKDAGLVKSLGVSNFNRR-QLELI
          LD.VDLYIIE..MA.KP.DEIYP..ENGKWLYHKSNLCATWE..EACKDAGLVKSLGVS.FN.R.QLELI
Retrocopy LDCVDLYIIEISMAPKPEDEIYPIGENGKWLYHKSNLCATWETSEACKDAGLVKSLGVSSFNSR>QLELI

Parental  LNKPGLKHKPVSNQVECHPYFTQPKLLKFCQQHDIVITAYSPLGTSRNPVWVNVSSPPLLKDALLNSLGK
          .N.PGLK.KPVSN.VECHPY.TQPKLLKFCQQHDIV..AYSPLGT.RNP.W.N.SSPP.LKDALL....K
Retrocopy QNNPGLKSKPVSNEVECHPYYTQPKLLKFCQQHDIVMIAYSPLGTTRNPTWTNMSSPPSLKDALL----K

Parental  RYNKTAAQIVLRFNIQRGVVVIPKSFNLERIKENFQIFDFSLTE
          R.NK..AQ..L.FNI..GVV.IPKSFN.E.IKEN.Q.FDFSLTE
Retrocopy RCNKITAQVILHFNIHQGVVIIPKSFNPEKIKENLQAFDFSLTE

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	0.00 RPM
SRP007412_kidney	0.00 RPM	0.13 RPM
SRP007412_liver	0.00 RPM	216.69 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_406 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_406 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_257
Pan troglodytes	retro_ptro_217
Gorilla gorilla	retro_ggor_307

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Homo sapiens	ENSG00000122787	1 retrocopy	retro_hsap_257,
Gorilla gorilla	ENSGGOG00000014684	1 retrocopy	retro_ggor_307,
Nomascus leucogenys	ENSNLEG00000013710	1 retrocopy	retro_nleu_860,
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	ENSPTRG00000019740	1 retrocopy	retro_ptro_217,
Rattus norvegicus	ENSRNOG00000013004	1 retrocopy	retro_rnor_2559,