RetrogeneDB ID: retro_ptro_1017

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:48170772..48172165(+)
• Located in intron of: ENSPTRG00000007072

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSPTRG00000020493
• Aliases: DCAF13, WDSOF1
• Description: DDB1 and CUL4 associated factor 13 [Source:HGNC Symbol;Acc:24535]

Sequence

>retro_ptro_1017
CAGTGGACAGAACTCACAGCGAAGAGCTCATGGAGTCCGGCCAGAAGAGCAACCAAGATGAGGATGAAGATACTGAGCCA
GAATCTGGACAATTATGTCTGTGAAACCAAGTTGGACTTACAGAGAGTTCTAAGAAACTATGATCCTACCTTACATCCTT
TTGAGGTCCCATGAGAATATGTAAGAGCTTTAAATGCTACCAAAATGGAATGAGTATTTGCAAAACCATTCCTTGCTTTG
CTGGATGGTCACCAAGATGGAGTCAGTTGCTTGGCAAAGCATCCAAAGAACCTGGCTACTGTCCTTTCTGGGGCGTGTGA
TGGAGAGGTTAGAATTTGGAACCTGACTCAACAGAAATGTATCCGTACAATACAAGCACATGAAGGCTTTGTATAAGGAA
TACGTACTCACTTTTGTGGGACTTCTTTTTTCACCGTTGGTGGTGACAAAACTGTGAAACAATGGAAAATGGATGGGCCA
GGCTATGGAGATGAGGAAGAACCATTACCTACAACATTAGGAAAGACAGTGTATACTGGGGTTTATCATCACTGTAAAGA
AGCTGTTTTTGCCACATGTGGACAGCAAGTAGACATTTGGGATGAATAAAGAACTAATCCTGTATGTTCAATGACCTGGG
GATTTGACAGTGTAAGTAGTGTTAAATTTAACCCAATCGAGACATTTCTCTTGGGAAGTTTGTGCGTCTGACAGGAATAT
AGTACTGTATGACATGAGGCAAGCTATTCCTTTGAAAAAGGTTATATTAGATATGAGAACAAATACAGTTTGTTGGAACC
CTATGGAAGCTTTCATTTTTACGGCAGCAAATGAAGACTATAACTTACATACTTTTGATATGTGTGCACCGAACACTCCT
GTAATGTTCCATATGGATCTTGTATCTGCAGTGCTTGACATGGATTACCCTCCCACTGGGAAAGAGTTTGTGTCTGCTAG
TTTCGATAAAGCTATTTGTATCTTTCCTATAGACAACAGTTGAAGCAGGGAGGTATATCACACAAAGCGAATGCAACATG
TTATCTGTGTAAAATGGACTTCTGACAGAAAGTATATTATGTGTGGATCTGATGAAATGAACATTTGCCTGTGGAAAGCT
AATGCTTCTGAAAAATTTGGTGTGCTTACATCATGAGAAAAAGCAGCTAAAGATTATAACTAGAAATTGAAGGAGAAATT
TCAGCATCATCCTCATATAAAATGTATAGCTTGTCATTGACATCTACCAAAATCTATCTACAGCCAGATTCAGGAACAGC
GCATCATGAAAGAAGCTCGTCGAAGAAAGGAAGTGAATCGTATTAAACACAGCAAGCCTGGATCTGTGCCAATTGTGTCA
GAGAAGAAGAAACACGTAGGGGCAGTTGTAAAA

Alignment

ORF - retro_ptro_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.88 %
• Parental protein coverage: 80.56 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RWAELVANSSWSPAGRATEMKVKMLSRNPDNYVRETKLDLQRVPRNYDPALHPFEVPREYVRALNATKLE
          .W.EL.A.SSWSPA.RAT.M..K.LS.N.DNYV.ETKLDLQRV.RNYDP.LHPFEVP.EYVRALNATK.E
Retrocopy QWTELTAKSSWSPARRATKMRMKILSQNLDNYVCETKLDLQRVLRNYDPTLHPFEVP*EYVRALNATKME

Parental  RVFAKPFLASLDGHRDGVNCLAKHPENLATVLSGACDGEVRIWNLTQRNCIRTIQAHEGFVRGICTRFCG
          .VFAKPFLA.LDGH.DGV.CLAKHP.NLATVLSGACDGEVRIWNLTQ..CIRTIQAHEGFV.GI.T.FCG
Retrocopy *VFAKPFLALLDGHQDGVSCLAKHPKNLATVLSGACDGEVRIWNLTQQKCIRTIQAHEGFV*GIRTHFCG

Parental  TSFFTVGDDKTVKQWKMDGPGYGDEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTNPICS
          TSFFTVG.DKTVKQWKMDGPGYGDEEEPL.T.LGKTVYTG..HH.KEAVFATCGQQVDIWDE.RTNP.CS
Retrocopy TSFFTVGGDKTVKQWKMDGPGYGDEEEPLPTTLGKTVYTGVYHHCKEAVFATCGQQVDIWDE*RTNPVCS

Parental  MTWGFDSISSVKFNPIETFLLGS-CASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANED
          MTWGFDS.SSVKFNPIETFLLGS.CASDRNIVLYDMRQA.PLKKVILDMRTNT.CWNPMEAFIFTAANED
Retrocopy MTWGFDSVSSVKFNPIETFLLGS>CASDRNIVLYDMRQAIPLKKVILDMRTNTVCWNPMEAFIFTAANED

Parental  YNLYTFDMRALDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSREVYHTKRMQHVIC
          YNL.TFDM.A..TPVM.HMD.VSAVLD.DY.PTGKEFVSASFDK.I.IFP.D.S.SREVYHTKRMQHVIC
Retrocopy YNLHTFDMCAPNTPVMFHMDLVSAVLDMDYPPTGKEFVSASFDKAICIFPIDNS*SREVYHTKRMQHVIC

Parental  VKWTSDSKYIMCGSDEMNIRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHYPHIKRIARHRHLPKSI
          VKWTSD.KYIMCGSDEMNI.LWKANASEK.GVLTS.EKAAKDYN.KLKEKFQH.PHIK.IA.H.HLPKSI
Retrocopy VKWTSDRKYIMCGSDEMNICLWKANASEKFGVLTS*EKAAKDYN*KLKEKFQHHPHIKCIACH*HLPKSI

Parental  YSQIQEQRIMKEARRRKEVNRIKHSKPGSVPIVSEKKKHVVAVVK
          YSQIQEQRIMKEARRRKEVNRIKHSKPGSVPIVSEKKKHV.AVVK
Retrocopy YSQIQEQRIMKEARRRKEVNRIKHSKPGSVPIVSEKKKHVGAVVK

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	0.07 RPM	13.12 RPM
SRP007412_cerebellum	0.11 RPM	15.59 RPM
SRP007412_heart	0.29 RPM	13.23 RPM
SRP007412_kidney	0.10 RPM	31.96 RPM
SRP007412_liver	0.13 RPM	13.49 RPM
SRP007412_testis	0.32 RPM	98.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1017 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1017 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1498
Gorilla gorilla	retro_ggor_1150
Pongo abelii	retro_pabe_1249

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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,