RetrogeneDB ID: retro_ggor_406

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:80328084..80328694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSGGOG00000003724
• Aliases: None
• Description: None

Sequence

>retro_ggor_406
GCAACTTTCCACTTGGCCCTCATCCAGCTTCAAGTTTCTTCATCAAATCAGATAACAACACTCGAGCTTGTAGCCTTGTC
CGGGAGACAGCAACACAAGGAGCCAAAATGGTTTCTTTGTTGGAATGCTTTAATTCTCCATATGGCACAAAATATTTTCC
TGAATATGCAGCGAAAATTCCTGGTAAATCCACACAGAAGGTTTCTGAAGTAGCAAGGGAATACAGCCTCACTAGAGGTT
CCATCCCTGAAGAGGATGCTGGGAAATTAGATAACACCTGTGCTGTGTTTGCACCTCATGGAACTTTACTAGTAAAGCAC
AGAAAGGTCCATCTGCTTAACACTGGTGTTCCTGGAAAAATGACGTTTCAAGAATCCACAATGTTGAGTCCGGGCAATGG
TTTCTCCACATTTGATACTCCTTACTGAAGAATGAGTCGGGGCATCTGCTGTGACACTGGTTTGCAGAGCTTGCACAAAT
CTACACACGGAAAGGCTGCCAGCTGTTGGTTTATCCAGGGGCTTTCAGTTTGACCACTGGACCAGCCCACTGGGAATTGC
TTCAGGCTCTTGATAATCAGGTGTATGTGGCCACATTCTCCTGCCCAAGA

Alignment

ORF - retro_ggor_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.24 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAFRLALIQLQISS-IKSDNVTRACSFIREAATQGAKIVSLPECFNSPYGTKYFPEYAEKIPGESTQKLS
          ..F.LALIQLQ.SS.IKSDN.TRACS..RE.ATQGAK.VSL.ECFNSPYGTKYFPEYA.KIPG.STQK.S
Retrocopy ATFHLALIQLQVSS<IKSDNNTRACSLVRETATQGAKMVSLLECFNSPYGTKYFPEYAAKIPGKSTQKVS

Parental  EVAKECSIYLIGVKGSIPEEDAGKLYNTCAVFGPDGTLLAKYRKIHLFDIDVPGKITFQESKTLSPGDSF
          EVA.E.S.......GSIPEEDAGKL.NTCAVF.P.GTLL.K.RK.HL....VPGK.TFQES..LSPG..F
Retrocopy EVAREYSL----TRGSIPEEDAGKLDNTCAVFAPHGTLLVKHRKVHLLNTGVPGKMTFQESTMLSPGNGF

Parental  STFDTPYCRVGLGICYDMR-FAELAQIYAQRGCQLLVYPGAFNLTTGPAHWELLQRSRAVDNQVYVATAS
          STFDTPY.R...GIC.D...FAELAQIY...GCQLLVYPGAF.LTTGPAHWELLQ...A.DNQVYVAT.S
Retrocopy STFDTPY*RMSRGICCDTG<FAELAQIYTRKGCQLLVYPGAFSLTTGPAHWELLQ---ALDNQVYVATFS

Parental  PAR
          ..R
Retrocopy CPR

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	0.05 RPM	12.42 RPM
SRP007412_cerebellum	0.00 RPM	5.87 RPM
SRP007412_heart	0.00 RPM	6.66 RPM
SRP007412_kidney	0.49 RPM	132.23 RPM
SRP007412_liver	0.03 RPM	133.26 RPM
SRP007412_testis	0.00 RPM	19.48 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_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_406 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_411
Pan troglodytes	retro_ptro_315
Macaca mulatta	retro_mmul_505
Callithrix jacchus	retro_cjac_3014

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406 ,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758, retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315,