RetrogeneDB ID: retro_ggor_1718

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:28114039..28114708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSGGOG00000009597
• Aliases: None
• Description: None

Sequence

>retro_ggor_1718
ATAGGAAATGGTGCCCTCGGTACTCAAGTGGAATGGGCACACTAAACTGGTGTCTCCCAGTTTAAGGACCGTGGGCTGAC
CAAGTTCTCCTTAGAATTGTAGACACTAAAGAGCAATCCCAGGACCATCGATTTGTCCAACAACAAGATGGACAACCTAC
CACTTTTGCTGATACAAAAGTTCACTCTGCTGAAGAACCTCCCCCTGAACAACATAAACTGGTCTGCCTAATGAGATTAT
GCAATCCTAAAAAAATTCTAGAGATGCTACGCCTAAACCGCAGTCACCTGAGAGAGCTGCCATCTACCTTTGGGCAACTC
TTTACCCTCAAGACCCTGAGCCTCTCTGGGAACCAACTGGGAGCGCTATCACCCAACTTTGTAGCCTAGGCCACCGGATG
TGGTGGATCTTTCCAAGAACCAGATCTGAAGTATACCTGACATAGTAGGAAAGCTGCAGGTCATCAAACTCATCCTCAAC
TGGAAGAAGATATCTCAGGTCTCAATAAAGATATCTGGCTGTCCTTGCCTTAAAATTCTTCACCTGGAAGAGAACTGTCT
TGATCTCAGCATGCTTTCACAGAGCATCTGCAGTGATTGCCAGATCTGTCCACTTGATATGGAAGGTAATCTTTTTAAAA
TAAACTTCAATAAGTACATGGAGAGGTTC

Alignment

ORF - retro_ggor_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 93.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGNSALRAHVETAQKTGVFQLKDRGLTEFPADLQKLTSNLRTIDLSNNKIESLPPLLIGKFTLLKSLSLN
          .GN.AL...VE.A..TGV.Q.KDRGLT.F...L..L.SN.RTIDLSNNK...LP.LLI.KFTLLK.L.LN
Retrocopy IGNGALGTQVEWAH*TGVSQFKDRGLTKFSLEL*TLKSNPRTIDLSNNKMDNLPLLLIQKFTLLKNLPLN

Parental  N-NKLTVLPDEICNLKK-LETLSLNNNHLRELPSTFGQLSALKTLSLSGNQLGALPP-QLCSLRHL-DVM
          N..KL..L....CN.KK.LE.L.LN..HLRELPSTFGQL..LKTLSLSGNQLGAL.P.QLCSL.H..DV.
Retrocopy N<HKLVCLM-RLCNPKKILEMLRLNRSHLRELPSTFGQLFTLKTLSLSGNQLGALSP<QLCSLGHR<DVV

Parental  DLSKNQIRSIPDSVGELQVIELNLNQNQISQISVKISCCPRLKILRLEENCLELSMLPQSILSDSQICLL
          DLSKNQI.SIPD.VG.LQVI.L.LN...ISQ.S.KIS.CP.LKIL.LEENCL.LSML.QSI.SD.QIC.L
Retrocopy DLSKNQI*SIPDIVGKLQVIKLILNWKKISQVSIKISGCPCLKILHLEENCLDLSMLSQSICSDCQICPL

Parental  AVEGNLFEIKKLRELEGY
          ..EGNLF.I......E..
Retrocopy DMEGNLFKINFNKYMERF

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	8.06 RPM
SRP007412_cerebellum	0.00 RPM	6.58 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.00 RPM	7.93 RPM
SRP007412_liver	0.00 RPM	4.99 RPM
SRP007412_testis	0.00 RPM	7.67 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_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1718 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2163
Pan troglodytes	retro_ptro_1650
Callithrix jacchus	retro_cjac_2819

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718 ,
Gorilla gorilla	ENSGGOG00000028048	1 retrocopy	retro_ggor_512,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,