RetrogeneDB ID: retro_ggor_2743

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:86585425..86586639(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000010312
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCAF4
• Ensembl ID: ENSGGOG00000003815
• Aliases: None
• Description: None

Sequence

>retro_ggor_2743
CCCCTCAGGAGGGAGAACATCCACCGAACGAAATGGAGAGCAAAAGACCGCGACTGCTCGAGGAAGCAGACAAGCAGAAA
AAGACAGTCAGAGTGGGACTCAATGCACCTTCCATGCTACGAAAGAACCAGCTAGGTTTCCTCAGATTCACCAGCTATTG
CCGTATAGCTCGCGAGCTGCGTGTAAGCTGCATGCAGAGGAAAAAGGTCCAGATTCATAGCTGGGATCCCTCCTCTTTGG
CAAGCGACCGATTTAACCGCATACTGGCGAATACCAACACTGACCAGCTCTTCACAGTGAACCCAGTCGAAGCTGGAGGC
TCCAAGTACGGCATCATCACCATGCGAGGCCTGACGACCCCTGAGCTCCGGGTATACCCGCACAAAAGCCTCTACGTCCC
TAATCGGAAGGTGAATTCTATGTGCTGGGCCTCACTGAATCACTTGGATTCCCACCTTCTGCTGTGCTTCGTGGGACTTG
CAGATACTCCAAGCTGTGCCGTGCTGCTCCCAGCGTCGCTGTTCATAGGTAGCTTCCCAGGAATGCGTCGGCCTGGCATG
CTTTGCAGTTTCCAGATCCCTGATGCCTGGTCCTGTGCCTGGTCCCTGAGCATCCACGCGTATCACTGCTTCAGTACAGG
CTTGTCTCAGCAGGTCCTGTTGACCAACGTGGTGACGGGACACCAGCAGTCATTTGGGACTAGCAGTGATGTCTTGGCCC
AGCAGTTTGCAATCATGACTCCTTTGCTGTTTAATGGCTGTCGCTCTGGGGAGATCTTTGGCATTGATCTGCGCTGTGGA
AATCAAGGCAGCGGGTGGAAGGCCATTTGCCTGTCCCATGATTCAGCAGTGACCTCTCTGCAAATCCTCCAAGATGGCCA
ATTCCTGGTGGCATCAGACATGACTGGAACTATCAAGCTGTGGGACTTGAGGGCCACTAAATGTGTAACACAGTACGAAG
GTCATGTGAATAACTCCGCCTACCTACCCCTGCATGTGAACGAAGAAGAAGGAGTCGTGGCGGCCGTGGGCCAGGACTGC
TACACGAGAATCTGGAGCCTCCGTCATGGCCACCTGCTCACAACCATACCCTCCCCATACCCCGCCTCGGAGAACGACAT
TCCCAGTGTGGCCTTCTCTTCTCGCCTCGGGGGCTTCCGAGGAGCACCAGGGCTGCTCATGGCTGTCCGGGAGGACCTTT
ATTGTTTCTCCTAC

Alignment

ORF - retro_ggor_2743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• 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..T.YC..A.ELR.SCM.RKK
Retrocopy PLRRENIHR<NEMESKRPRLLEEADKQKKTVRVGLNAPSMLRKNQLGFLRFTSYCRIARELRVSCMQRKK

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

Parental  SVCWASLNHLDSHILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANN
          S.CWASLNHLDSH.LLC..GLA.TP.CA.LLPASLF..S.PG..RPGMLCSF.IP.AWSCAWSL.I.A..
Retrocopy SMCWASLNHLDSHLLLCFVGLADTPSCAVLLPASLFIGSFPGMRRPGMLCSFQIPDAWSCAWSLSIHAYH

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

Parental  HDSAVTSVRILQDEQYLMASDMAGKIKLWDLRTTKHVRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYT
          HDSAVTS..ILQD.Q.L.ASDM.G.IKLWDLR.TK.V.QYEGHVN..AYLPLHV.EEEG...AVGQDCYT
Retrocopy HDSAVTSLQILQDGQFLVASDMTGTIKLWDLRATKCVTQYEGHVNNSAYLPLHVNEEEGVVAAVGQDCYT

Parental  RIWSLHDARLLRTIPSPYPASKADIPSVAFSSRLGGSRGAPGLLMAVGQDLYCYSY
          RIWSL....LL.TIPSPYPAS..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	15.78 RPM
SRP007412_cerebellum	0.00 RPM	5.04 RPM
SRP007412_heart	0.00 RPM	1.16 RPM
SRP007412_kidney	0.00 RPM	9.98 RPM
SRP007412_liver	0.00 RPM	3.85 RPM
SRP007412_testis	10.88 RPM	10.46 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2743 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_92
Pan troglodytes	retro_ptro_2774
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,