RetrogeneDB ID: retro_ggor_2143

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:192652677..192653353(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSGGOG00000005172
• Aliases: None
• Description: None

Sequence

>retro_ggor_2143
CATCACTCCTGGATAATAATGCTCACATGTGCATTTTTGGCCTACAAAGTAGATAAACTGAATGTATCTAGTCCCCAATT
TGTTGGAAACCTTCGGGAGAGTTCTCTCGTACAGGAGGAGACACTTGAACAGAGTTTGGAATATGAACTACCTTTTATAC
AGCAATGTAAATTTCCATCTGACTGTCCACATCCCCTATAGACCACTGGAGTGCTTCCTCACTGATTTAAAGACTTACTA
TGCAATGCTGGAGAATCCAGACATTTTGAGGAAAACAGATGATGAACTTCTTAATAGAATCACACTGATGGCTGCTTACT
GTTTATACACACCTTCCCAAATTGCCCTGCCTGCCATTTTATCCAGTGTCTTCAGGACTGGAATTACTATGGAAAGTTAT
TTATTGGACAGTCTGATGTTGAGAGAGAACAGAACTTGCTTGTCACAGTTACGAGATATAGTGAAAAGCATGAGAAATTG
AGTAAAAAAGTATGTACCACCCAGATCTGAAGAAGCTGCTGTTCTGAAACTGAAGTTGGAGCAATGTCATTCTGCTGAGC
TTGCACTTAATGTAATTATGAAGAAGAGGAAAGGCTGTGAAGATAATGATGATATCTCAAAGAAATCCAGACATGAGGAG
GAAGAATACACTGATGATGACCTGGTAGACTCTCTC

Alignment

ORF - retro_ggor_2143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.55 %
• Parental protein coverage: 69.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQ-LNFHLIVHNPYRPF
          .H..IIMLTCAFLA.KVD..NVSSPQFVGNLRES.L.QE..LEQ.LEYEL..IQQ..NFHL.VH.PYRP.
Retrocopy HHSWIIMLTCAFLAYKVDKLNVSSPQFVGNLRESSLVQEETLEQSLEYELPFIQQ>VNFHLTVHIPYRPL

Parental  EGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLM
          E.FL.DLKT.Y..LENP.ILRKT.D..LNRI.L..AY.LYTPSQIAL.AILSS..R.GITMESYL..SLM
Retrocopy ECFLTDLKTYYAMLENPDILRKTDDELLNRITLMAAYCLYTPSQIALPAILSSVFRTGITMESYLLDSLM

Parental  LKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKS
          L.ENRTCLSQL.DI.KSMRN.VKKY.PPRSEE.AVLK.KLE.CHSAELALNVI.KKRKG.ED.D..SKKS
Retrocopy LRENRTCLSQLRDIVKSMRN*VKKYVPPRSEEAAVLKLKLEQCHSAELALNVIMKKRKGCEDNDDISKKS

Parental  KHEEEEWTDDDLVESL
          .HEEEE.TDDDLV.SL
Retrocopy RHEEEEYTDDDLVDSL

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	10.45 RPM
SRP007412_cerebellum	0.00 RPM	8.08 RPM
SRP007412_heart	0.00 RPM	3.03 RPM
SRP007412_kidney	0.00 RPM	17.09 RPM
SRP007412_liver	0.00 RPM	20.89 RPM
SRP007412_testis	0.00 RPM	58.64 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_2143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2143 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3128
Pan troglodytes	retro_ptro_2116
Pongo abelii	retro_pabe_2584
Macaca mulatta	retro_mmul_1991

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143 ,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,