RetrogeneDB ID: retro_ggor_423

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:119613981..119615140(-)
• Located in intron of: ENSGGOG00000012864

Retrocopy information

• Ensembl ID: ENSGGOG00000027658
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAP1L4
• Ensembl ID: ENSGGOG00000013223
• Aliases: None
• Description: None

Sequence

>retro_ggor_423
ATGGCAGATAACAGTTTTTCAGATGGGGTTCCTTCAGATTTCGTGGAAGCTGCTAAAAGTGCAAGTAAGACGGAAAAGCT
CACGGATCAGGTGATGCAGAATCCTGGAGTTTTGGCAGCTTTACAGGAGCGACTTGACAATGCTCCTCACACCCCTTCCA
GCTACATTGAAACTTTACCTAAAGCAGTAAAAAGAAGAATTAATGCATTGAAACAAATTCAGGTGAGATGCGCTCATATA
GAAGCCAAGTTCCATGAAGAAGTTCATGACTTGGAAAGAAAATATGCAGCATTGTACCAGCCTCTCTTTGACGAGAGAAG
AGAATTTATCACCGGTAATGTTGAACCAACTTCTGATATGGAATCAGAATGGCACAGTGAAAATGAAGAGGAGGAGAAAT
TGGCTGCAGACAGGAAAAATAAAGTAGTCATAACAGAAAAAGCAGCAGCAACAGCTGAAGAGCCAAATCCCAAAGGAATT
CCAGAGTTCTGGTTTACCATCTTTAGAAATGTAGATATGCTAAGTGAATTAGTCCAGGAATATGATGAGCCAATCTTGAA
ACACCTGCAGGATATTAAAGTGAAGTTTTCTGACCCTGGACAGCCTATGTCTTTCATATTAAGAGTTCCACTTTCAACCC
AACGACTGCTTTGCCAATTCAGTCCTGACAAAAACCTGCAAGATGAAATCAGAACCAGGTAAGGCTGATCCCTTTTCATT
TGCAGGTCCTGAGATCATGGACTGCGACGGGTGTACTATTGACTGGAAGAAAGGAAAGAATGTTACTGTCAAAACCATCA
AGAAAAAGCAGAAGCGTAAGGGTCCAGGCACTGCTAGAACAATTACCAAACAAGTATCCAATGAGTCATTTTTCAACTTC
TTCAATCCACTGAAAGCATCTGGGGACAGAGAATCACTGGATAAAGATTCTGAATTCGTATTAGCCTCTGATTTTGAAAT
TGGACACTTTTTCCGTGAGCAGATAGTCCCACAGGCTGTGCTGTACTTCGCTGGGGAGGCCTTAGAGGATGATGACAATT
TTGACGAAGGTGAAGAAGAAGAGGACGAATTAGAAGGTGACAAGGAGGGAGAAGATGAGGATGAGGTGGAAATTAATCCC
AACAAGGAACCCAGCCAGCCGGCGGAATGCAAGCAGCAG

Alignment

ORF - retro_ggor_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADHSFSDGVPSDSVEAAKNASNTEKLTDQVMQNPRVLAALQERLDNVPHTPSSYIETLPKAVKRRINAL
          MAD.SFSDGVPSD.VEAAK.AS.TEKLTDQVMQNP.VLAALQERLDN.PHTPSSYIETLPKAVKRRINAL
Retrocopy MADNSFSDGVPSDFVEAAKSASKTEKLTDQVMQNPGVLAALQERLDNAPHTPSSYIETLPKAVKRRINAL

Parental  KQLQVRCAHIEAKFYEEVHDLERKYAALYQPLFDKRREFITGDVEPT-DAESEWHSENEEEEKLAGDMKN
          KQ.QVRCAHIEAKF.EEVHDLERKYAALYQPLFD.RREFITG.VEPT.D.ESEWHSENEEEEKLA.D.KN
Retrocopy KQIQVRCAHIEAKFHEEVHDLERKYAALYQPLFDERREFITGNVEPTSDMESEWHSENEEEEKLAADRKN

Parental  KVVVTEKEAATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQPMSFVL-EF
          KVV.TEK.AATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQPMSF.L.EF
Retrocopy KVVITEKAAATAEEPNPKGIPEFWFTIFRNVDMLSELVQEYDEPILKHLQDIKVKFSDPGQPMSFIL>EF

Parental  HFEPNDYFTNSVLTKTYKMKSEPDKADPFSFEGPEIVDCDGCTIDWKKGKNVTVKTIKKKQKHKGRGTVR
          HF.PND.F.NSVLTKT.KMKSEP.KADPFSF.GPEI.DCDGCTIDWKKGKNVTVKTIKKKQK.KG.GT.R
Retrocopy HFQPNDCFANSVLTKTCKMKSEPGKADPFSFAGPEIMDCDGCTIDWKKGKNVTVKTIKKKQKRKGPGTAR

Parental  TITKQVPNESFFNFFNPLKASGDGESLDEDSEFTLASDFEIGHFFRERIVPRAVLYFTGEAIEDDDNFEE
          TITKQV.NESFFNFFNPLKASGD.ESLD.DSEF.LASDFEIGHFFRE.IVP.AVLYF.GEA.EDDDNF.E
Retrocopy TITKQVSNESFFNFFNPLKASGDRESLDKDSEFVLASDFEIGHFFREQIVPQAVLYFAGEALEDDDNFDE

Parental  GEEGEEEELEGDEEGEDEDDAEINPKKEPSQPAECKQQ
          GEE.EE.ELEGD.EGEDED..EINP.KEPSQPAECKQQ
Retrocopy GEE-EEDELEGDKEGEDEDEVEINPNKEPSQPAECKQQ

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	0.29 RPM	115.09 RPM
SRP007412_cerebellum	0.04 RPM	104.92 RPM
SRP007412_heart	0.13 RPM	60.60 RPM
SRP007412_kidney	0.37 RPM	98.91 RPM
SRP007412_liver	0.11 RPM	51.33 RPM
SRP007412_testis	0.52 RPM	270.91 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_423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_423 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_438
Pan troglodytes	retro_ptro_192
Pongo abelii	retro_pabe_288

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000205531	1 retrocopy	retro_hsap_438,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Gorilla gorilla	ENSGGOG00000013223	1 retrocopy	retro_ggor_423 ,
Nomascus leucogenys	ENSNLEG00000010841	1 retrocopy	retro_nleu_1876,
Oryctolagus cuniculus	ENSOCUG00000005624	1 retrocopy	retro_ocun_384,
Pongo abelii	ENSPPYG00000002938	1 retrocopy	retro_pabe_288,
Pan troglodytes	ENSPTRG00000028747	1 retrocopy	retro_ptro_192,