RetrogeneDB ID: retro_ggor_2346

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:62964072..62964741(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC59
• Ensembl ID: ENSGGOG00000006310
• Aliases: None
• Description: None

Sequence

>retro_ggor_2346
ATGACTATTCTCCCGTCAGATTTCTGTGGCCTCACACACCTGGCGAAGCTAGACCTTAGAAAGAACAAGCCCCAGCACCC
ACCGGCGGACTTGGGCCGTTTGGTCAACCTCCAGCACCTGGCGCTCCTCAACAACAAGCTGGTCACCTTGTCTGTCAGCT
TTGCTCAGCTGAAGAACCTGAAGTGGCTGGACCTGAAGGATAACCTCTGGATCCCGGCCTGGCCAAGGTGGCAGGCGACT
GCTTGGGTGAGAAGCCATGGAAACAGCATGCAAACAACGCGTCACAGCACATGAAGGTTGTGCAGGCAGACCACAAGTAG
GAGAGGCAGCAGGGTTGGAAGTAGAACCAGAGGCAGAGGAGAAGTATGAGGCAAAGCAGCGAGCTAAGGAAGCTCAGGAG
AGGAAATGCAGAAGCGGGAGAAGGCAGAAGAGAAGGAGTGCCGGAGAAAGCAGTATGATGCCCTCAAAGCAGCCAAGTGG
GAGCAGATGATACCTACCAAGGAAACAAATTAGGCCCCCAAATCTAAGTCCGAATCCTGCCCCTGCAAGCCACTCCCCCG
GAAGCACACTCATTTCTGGGCTGTGCTGAAACTGCTGCTGCTGCTGCTGTTTTGTGCAGCGGGAGGGCTGGTTGCTGGTC
CAGTGACACAGCTACAGCAGCTGCCCCTT

Alignment

ORF - retro_ggor_2346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.74 %
• Parental protein coverage: 73.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTTLPSDFCGLTHLVKLDLSKNKLQQLPADFGRLVNLQHLDLLNNKLVTLPVSFAQLKNLKWLDLKDN-P
          .T.LPSDFCGLTHL.KLDL.KNK.Q..PAD.GRLVNLQHL.LLNNKLVTL.VSFAQLKNLKWLDLKDN.P
Retrocopy MTILPSDFCGLTHLAKLDLRKNKPQHPPADLGRLVNLQHLALLNNKLVTLSVSFAQLKNLKWLDLKDN<P

Parental  LDPVLAKVAGDCLDEKQCKQCANKVLQHMKAVQADQERERQR-RLEVEREAEKKREAKQRAKEAQER-EL
          LDP.LAKVAGDCL.EK..KQ.AN...QHMK.VQAD...ERQ...LEVE.EAE.K.EAKQRAKEAQER.E.
Retrocopy LDPGLAKVAGDCLGEKPWKQHANNASQHMKVVQADHK*ERQQ<GLEVEPEAEEKYEAKQRAKEAQER<EM

Parental  RKREKAEEKERRRKEYDALKAAKREQEKKPKKEANQAPKSKSGSRPRKPPPRKHTRSWAVLKLLLLLLLF
          .KREKAEEKE.RRK.YDALKAAK.EQ...P.KE.N.APKSKS.S.P.KP.PRKHT..W............
Retrocopy QKREKAEEKECRRKQYDALKAAKWEQ-MIPTKETN*APKSKSESCPCKPLPRKHTHFWXXXXXXXXXXFC

Parental  GVAGGLVACRVTELQQQPL
          ...G.LVA..VT.LQQ.PL
Retrocopy AAGG-LVAGPVTQLQQLPL

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	59.41 RPM
SRP007412_cerebellum	0.00 RPM	40.66 RPM
SRP007412_heart	0.00 RPM	13.04 RPM
SRP007412_kidney	0.00 RPM	56.30 RPM
SRP007412_liver	0.00 RPM	37.11 RPM
SRP007412_testis	0.00 RPM	115.51 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_2346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2346 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3479
Pan troglodytes	retro_ptro_2985
Pongo abelii	retro_pabe_2874

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346 ,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687, retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931,