RetrogeneDB ID: retro_pabe_1249

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:47568294..47569629(+)
• Located in intron of: ENSPPYG00000006473

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_1249
ATGAGGATGAAGATACTGAGCCAGAATCTGGACAATTATGTCTGTGAAACCAAGTTGGACTTACAGAGAGTTCCAAGAAA
CTGTGATCCTACCTTACATCCTTTTGAGGTCCCATGAGAATATGTAAGAGCTTTAAATGCTACCAAAATGGAATGAGTAT
TTGCAAAACCATTCCTTGCTTTGCTGGATGGTCACCAAGATGGAGTCAGTTGCTTGGCAAAGCATCCAAGGAACCTGGGT
ACTGTCCTTTCTGGGCGTGTGGTGGAGAGGTTAGAATTTGGAACCTGACTCAACAGAAATGTATCCGTACAATACAAGCA
CATGAAGGCTTTGTATAAGGAATATGTACTCACTTTTGTGGGACTTCTTTTTTCACTGTTGGTGGTGACAAAACTGTGAA
ACAATGGAAAATGGATGGGCCAGGCTATGGAGATGAGGAAGAACCATTACATACAACATTAGGAAAGACAGTGTATACTG
GGGTTTATCATCACTGGAAAGAAGCTGCTTTTGCCACATGTGGACAGCAAGTAGACGTTTGGGATGAACAAAGAACTAAT
CCTATATGTTCAATGACCTGGGGATTTGACAGTGTAAGTAGTGTTAAATTTAACCCAATTGAGACATTTCTCTTGGGAAG
TTTGTGCGTCTGACAGGAATATAGTACTGTACAACATGAGGCAAGCTACTCCTTTGAAAAAGGTTATCTTAGATATGAGA
ACAAATACAGTCTGTTGGAACCCTATGGAAGCTTTCATTTTTACAGCAGCAAATGAAGACTATAACTTACATACTTTTGA
TATGTGTGCACTGGACACTCCTGTAATGTTCCATATGGATCATGTATCTGCAGTGCTTGACATGGATTACCCTCCCACTG
GGAAAGAGTTTGTGTCTGCTAGTTTCGATAAAGCTATTTGAATCTTTCCTATAGACAAAAGTTGAAGCAGGGAGGTATAT
CACACAAAGTGAATACAACATGTTATCTGTGTAAAATGGACTTCTGACAGCAAGTATATTATGTGTGGATCTGATGAAAT
GAACATTTGCCTGTGGAAAGCTAATGCTTCTGAGAAATTTGGTGTGCTTACATCACGAGAAAAAGCAGCCAAAGATTATA
ACTAGAAATTGAAGGAGAAATTTCAGCATCATCCTCATATAAAATATATAGCTTGTCATCGACATCTACCAAAATCTATC
TACAGCCAGATTCAGGAACAGCGCATCATGAAAGAAGCTCGTCGAAGAAAGGAAGTAAATTGTATTAAACACAGCAAGCC
TGGATCTGTGCCAGTTGTGTCAGAGAAGAAGAAACATGTAGGGGCAGTTGTAAAA

Alignment

ORF - retro_pabe_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKVKMLSRNPDNYVRETKLDLQRVPRNYDPTLHPFEVPREYVRALNATKLERVFAKPFLASLDGHRDGVN
          M..K.LS.N.DNYV.ETKLDLQRVPRN.DPTLHPFEVP.EYVRALNATK.E.VFAKPFLA.LDGH.DGV.
Retrocopy MRMKILSQNLDNYVCETKLDLQRVPRNCDPTLHPFEVP*EYVRALNATKME*VFAKPFLALLDGHQDGVS

Parental  CLAKHPKNLATVLSG-ACDGEVRIWNLTQRNCIRTIQAHEGFVRGICTRFCGTSFFTVGDDKTVKQWKMD
          CLAKHP.NL.TVLSG.AC.GEVRIWNLTQ..CIRTIQAHEGFV.GICT.FCGTSFFTVG.DKTVKQWKMD
Retrocopy CLAKHPRNLGTVLSG<ACGGEVRIWNLTQQKCIRTIQAHEGFV*GICTHFCGTSFFTVGGDKTVKQWKMD

Parental  GPGYGDEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTNPVCSMTWGFDSISSVKFNPIET
          GPGYGDEEEPLHT.LGKTVYTG..HHWKEA.FATCGQQVD.WDEQRTNP.CSMTWGFDS.SSVKFNPIET
Retrocopy GPGYGDEEEPLHTTLGKTVYTGVYHHWKEAAFATCGQQVDVWDEQRTNPICSMTWGFDSVSSVKFNPIET

Parental  FLLGS-CASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRALDTPVMVH
          FLLGS.CASDRNIVLY.MRQATPLKKVILDMRTNT.CWNPMEAFIFTAANEDYNL.TFDM.ALDTPVM.H
Retrocopy FLLGS>CASDRNIVLYNMRQATPLKKVILDMRTNTVCWNPMEAFIFTAANEDYNLHTFDMCALDTPVMFH

Parental  MDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSREVYHTKRMQHVICVKWTSDSKYIMCGSDEMN
          MDHVSAVLD.DY.PTGKEFVSASFDK.I.IFP.DKS.SREVYHTK..QHVICVKWTSDSKYIMCGSDEMN
Retrocopy MDHVSAVLDMDYPPTGKEFVSASFDKAI*IFPIDKS*SREVYHTK*IQHVICVKWTSDSKYIMCGSDEMN

Parental  IRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHYPHIKRIARHRHLPKSIYSQIQEQRIMKEARRRKE
          I.LWKANASEK.GVLTSREKAAKDYN.KLKEKFQH.PHIK.IA.HRHLPKSIYSQIQEQRIMKEARRRKE
Retrocopy ICLWKANASEKFGVLTSREKAAKDYN*KLKEKFQHHPHIKYIACHRHLPKSIYSQIQEQRIMKEARRRKE

Parental  VNRIKHSKPGSVPIVSEKKKHVVAVVK
          VN.IKHSKPGSVP.VSEKKKHV.AVVK
Retrocopy VNCIKHSKPGSVPVVSEKKKHVGAVVK

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	11.06 RPM
SRP007412_cerebellum	0.24 RPM	21.52 RPM
SRP007412_heart	0.09 RPM	11.41 RPM
SRP007412_kidney	0.23 RPM	33.41 RPM
SRP007412_liver	0.21 RPM	16.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1249 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1249 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1498
Pan troglodytes	retro_ptro_1017
Gorilla gorilla	retro_ggor_1150

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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,