RetrogeneDB ID: retro_ptro_2774

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:86046253..86047467(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000020402
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAF4
• Ensembl ID: ENSPTRG00000006507
• Aliases: DCAF4, WDR21A
• Description: None

Sequence

>retro_ptro_2774
CCCCTCAGGAGGGAGAACATCCACCGAACGAAATGGAGAGCAAAAGACCGCGACTGCTCGAGGAAGCAGACAAGCAGAAA
AAGACAGTCAGAGTGGGACTCAATGCACCTTCCATGCTACGAAAGAACCAGCTAGGTTTCCTCAGATTTACCAACTATTG
CCGTATAGCTCGCGAGCTGCGTGTAAGCTGCATGCAGAGGAAAAAGGTCCAGATTCATAGCTGGGATCCCTCCTCTTTGG
CAAGCGACCGATTTAACCGCATACTGGCGAATACCAACACTGACCAGCTCTTCACAGTGAACCAAGTCGAAGCTGGAGGC
TCCAAGTACGGCATCATCACCATGCGAGGCCTGACGACCCCTGAGCTCCGGGTATACCCGCACAAAAGCCTCTACGTCCC
TAATCGGAAGGTGAATTCTATGTGCTGGGCCTCACTGAATCACTTGGATTCCCACCTTCTGCTGTGCTTCGTGGGACTTG
CAGATACTCCAAGCTGTGTCGTGCCGCTCCCAGCGTCGCTGTTCATAGGTAGCTTCCCAGGAATGCGTCGGCCTGGCATG
CTTTGCAGTTTCCAGATCCCTGATGCCTGGTCCTGTGCCTGGTCCCTGAGCATCCACGCGTATCACTGCTTCAGTACAGG
CTTGTCTCAGCAGGTCCTGTTGACCAACGTGGTGACGGGACACCAGCAGTCATTTGGGACTAGCAGTGATGTCTTGGCCC
AGCAGTTTGCAATCATGACTCCTTTGCTGTTTAATGGCTGTCGCTCTGGGGAGATCTTTGGCATTGATCTGCGCTGTGGA
AATCAAGGCAGCGGGTGGAAGGCCATTTGCCTGTCCCATGATTCAGCAGTGACCTCTCTGCAAATCCTCCAAGATGGCCA
ATTCCTGGTGTCATCAGACGTGACTGGAACTATCAAGCTGTGGGACTTGAGGGCCACTAAATGTGTAACACAGTACGAAG
GTAATGTGAATAACTCCGCCTACCTACCCCTGCATGTGAACAAAGAAGAAGGAGTCGTGGCGGCCGTGGGCCAGGACTGC
TACACGAGAATCTGGAGCCTCCGTCATGGCCACCTGCTCACAACCATACCCTCCCCATACCCCGCCTCGGAGAACGACAT
TCCCAGTGTGGCCTTCTCTTCTCGCCTCGGGGGCTTCCGAGGAGCACCAGGGCTGCTCATGGCTGTCCGGGAGGACCTTT
ATTGTTTCTCCTAC

Alignment

ORF - retro_ptro_2774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.91 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PLTKESIRQ-KEMESKRLRLLQEEDRRKKIARMGFNASSMLRKSQLGFLNVTNYCHLAHELRLSCMERKK
          PL..E.I....EMESKR.RLL.E.D..KK..R.G.NA.SMLRK.QLGFL..TNYC..A.ELR.SCM.RKK
Retrocopy PLRRENIHR<NEMESKRPRLLEEADKQKKTVRVGLNAPSMLRKNQLGFLRFTNYCRIARELRVSCMQRKK

Parental  VQIRSMDPSALASDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVN
          VQI.S.DPS.LASDRFN.ILA.TN.D.LFTVN.V..GGSKYGII....L.TP.L.V..H..LY..NRKVN
Retrocopy VQIHSWDPSSLASDRFNRILANTNTDQLFTVNQVEAGGSKYGIITMRGLTTPELRVYPHKSLYVPNRKVN

Parental  SVCWASLNHLDSHILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANN
          S.CWASLNHLDSH.LLC..GLA.TP.C...LPASLF..S.PG..RPGMLCSF.IP.AWSCAWSL.I.A..
Retrocopy SMCWASLNHLDSHLLLCFVGLADTPSCVVPLPASLFIGSFPGMRRPGMLCSFQIPDAWSCAWSLSIHAYH

Parental  CFSTGLSRRVLLTNVVTGHRQSFGTNSDVLAQQFALMAPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLF
          CFSTGLS..VLLTNVVTGH.QSFGT.SDVLAQQFA.M.PLLFNGCRSGEIF.IDLRCGNQG.GWKA..L.
Retrocopy CFSTGLSQQVLLTNVVTGHQQSFGTSSDVLAQQFAIMTPLLFNGCRSGEIFGIDLRCGNQGSGWKAICLS

Parental  HDSAVTSVRILQDEQYLMASDMAGKIKLWDLRTTKCVRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYT
          HDSAVTS..ILQD.Q.L..SD..G.IKLWDLR.TKCV.QYEG.VN..AYLPLHV..EEG...AVGQDCYT
Retrocopy HDSAVTSLQILQDGQFLVSSDVTGTIKLWDLRATKCVTQYEGNVNNSAYLPLHVNKEEGVVAAVGQDCYT

Parental  RIWSLHDARLLRTIPSPYAASKADIPSVAFSSRLGGSRGAPGLLMAVGQDLYCYSY
          RIWSL....LL.TIPSPY.AS..DIPSVAFSSRLGG.RGAPGLLMAV..DLYC.SY
Retrocopy RIWSLRHGHLLTTIPSPYPASENDIPSVAFSSRLGGFRGAPGLLMAVREDLYCFSY

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	5.72 RPM
SRP007412_cerebellum	0.00 RPM	4.19 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.00 RPM	5.78 RPM
SRP007412_liver	0.00 RPM	4.22 RPM
SRP007412_testis	2.95 RPM	11.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2774 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2774 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2774 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_92
Gorilla gorilla	retro_ggor_2743
Macaca mulatta	retro_mmul_264

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013878	1 retrocopy	retro_cpor_293,
Homo sapiens	ENSG00000119599	2 retrocopies	retro_hsap_101, retro_hsap_92,
Gorilla gorilla	ENSGGOG00000003815	2 retrocopies	retro_ggor_2026, retro_ggor_2743,
Macaca mulatta	ENSMMUG00000003625	2 retrocopies	retro_mmul_152, retro_mmul_264,
Nomascus leucogenys	ENSNLEG00000002449	2 retrocopies	retro_nleu_1912, retro_nleu_833,
Pan troglodytes	ENSPTRG00000006507	2 retrocopies	retro_ptro_2774 , retro_ptro_46,