RetrogeneDB ID: retro_pabe_3211

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:16706709..16707520(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSPPYG00000018809
• Aliases: DCAF13, WDSOF1
• Description: DDB1- and CUL4-associated factor 13 [Source:RefSeq peptide;Acc:NP_001126898]

Sequence

>retro_pabe_3211
GTGAAGGTGAAGATGTTGAGCTGGAATCTGGACAACTATGTCCACAAAACCAAGTTGGACTTACAGATTGTTCCAAGAAA
CTATGATCCTACCTTACATCCTTTTGAGATCCTGCAAGAATGTGTAAGAGTTTTAAATGCTACCAAACTGGAAGGAGTAT
TTGCAAAACCATGCCTGGCTTGGCTGGATGGTCACGAGATGGAGTCAGTTGCTTGGCAAAGCATCCAAAGAGACTGGCTA
CTGTCCTTTCTGGGGGATGTGATGGAGCAGTTAGAATTTGGAACCTGACTCAACTGAAATGTATCCGTATAATACAAGCA
CATGAAGGTTTTGTACAAGGAATACATACTCACTTTTGTGGGACTTCTTTTTTCACTGTTGGTGATGACAAAACTGTGAA
GCAGTGGAAAATGGATGGGCCAGGCTATGGCGAGGAGGAAGAGCCATTACATACAATATTGGGAAAGACAGTGTATACTG
GGATTGATCATCACTGGAAAGAAGCTGTTTTTGCCACATGTGGACAGCAAGTAGACATTTGGGATGAACTAATAACTAAT
CCTATATGTTCACGACCTGGAGATTTGACAGTATATGTAGTGGTAAATTTAATGCAATTGAGACATTTATCTTGGGGAGT
TGCGCTTCTGACAGGACTATAGCACTGTATGATATGAGGCAAGCTACTCCTCTGAAAAAGGTTATCTTAAATATGAGAAC
AAATACAATCTGTTGAAACCCTATGGAAGCTTTCATTTTTATGGCAGCAAATGATGATTATAACTTACTTACTTTTGATA
TGCATGCACTC

Alignment

ORF - retro_pabe_3211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.88 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKVKMLSRNPDNYVRETKLDLQRVPRNYDPTLHPFEVPREYVRALNATKLERVFAKPFLASLDGH-RDGV
          .KVKMLS.N.DNYV..TKLDLQ.VPRNYDPTLHPFE...E.VR.LNATKLE.VFAKP.LA.LDGH.RDGV
Retrocopy VKVKMLSWNLDNYVHKTKLDLQIVPRNYDPTLHPFEILQECVRVLNATKLEGVFAKPCLAWLDGH<RDGV

Parental  NCLAKHPKNLATVLSGACDGEVRIWNLTQRNCIRTIQAHEGFVRGICTRFCGTSFFTVGDDKTVKQWKMD
          .CLAKHPK.LATVLSG.CDG.VRIWNLTQ..CIR.IQAHEGFV.GI.T.FCGTSFFTVGDDKTVKQWKMD
Retrocopy SCLAKHPKRLATVLSGGCDGAVRIWNLTQLKCIRIIQAHEGFVQGIHTHFCGTSFFTVGDDKTVKQWKMD

Parental  GPGYGDEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTNPVCS-MTWGFDSISSVKFNPIE
          GPGYG.EEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDE..TNP.CS..TW.FDSI.S.KFN.IE
Retrocopy GPGYGEEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDELITNPICS<TTWRFDSICSGKFNAIE

Parental  TFLLGSCASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRAL
          TF.LGSCASDR.I.LYDMRQATPLKKVIL.MRTNTIC.NPMEAFIF.AAN.DYNL.TFDM.AL
Retrocopy TFILGSCASDRTIALYDMRQATPLKKVILNMRTNTIC*NPMEAFIFMAANDDYNLLTFDMHAL

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	0.11 RPM	11.06 RPM
SRP007412_cerebellum	0.12 RPM	21.52 RPM
SRP007412_heart	0.09 RPM	11.41 RPM
SRP007412_kidney	0.10 RPM	33.41 RPM
SRP007412_liver	0.00 RPM	16.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3211 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211 ,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,