RetrogeneDB ID: retro_ggor_1368

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:12074201..12074687(+)
• Located in intron of: ENSGGOG00000016040

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1B
• Ensembl ID: ENSGGOG00000025604
• Aliases: None
• Description: None

Sequence

>retro_ggor_1368
ATTAAAAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATACACGCCGAAAATGCCATCCGCCAGAAGAACCAGGC
GGTGAATTTCTTGAGAATGAGTGCGCGAGTCGATGCAGTGGCTGCCAGGGTCCAGACGGCGGTGACCATGGGCAAGGTGA
CCAAGTCGATGGCTGGTGTAGTTAAGTCGATGGATGCGACATTGAAGACCATGAATCTGGAGAAGATTTCTGCTTTGATG
GACAAATTCGAGCATCAGTTTGAGACTCTGGACGTCCAGACGCAGCAAATGGAAGACACGATGAGCAGCACGACGACGCT
CACCACTCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGATGAGGCGGGCCTCGACCTCAACATGGAGCTGC
CGCAGGGCCAGACCGGCTCCGTGGGCACGAGCGTGGCTTCGGCGGAGCAGGATGAACTGTCTCAGAGACTGGCCCGCCTT
CGGGAT

Alignment

ORF - retro_ggor_1368 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKQAIQKGNKEAARTHAENAIHQKNQAIDFLRMSARVGAVAVRVQNAVTMGRVRLKSQRSIVKSVGASLR
          .K.AIQKGN.E.AR.HAENAI.QKNQA..FLRMSARV.AVA.RVQ.AVTMG.V..KS....VKS..A.L.
Retrocopy IKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVDAVAARVQTAVTMGKVT-KSMAGVVKSMDATLK

Parental  SRTLKRQTSALMNKFEHQFETLDIQTQQMEDKMSSSTTLITPQNQMDMLLQEMADEGSLDLNMQLPQGQI
          ...L....SALM.KFEHQFETLD.QTQQMED.MSS.TTL.TPQNQ.DMLLQEMADE..LDLNM.LPQGQ.
Retrocopy TMNLEK-ISALMDKFEHQFETLDVQTQQMEDTMSSTTTLTTPQNQVDMLLQEMADEAGLDLNMELPQGQT

Parental  DSLGTNVASMEQDKLSQRLALLHD
          .S.GT.VAS.EQD.LSQRLA.L.D
Retrocopy GSVGTSVASAEQDELSQRLARLRD

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	25.46 RPM	0.00 RPM
SRP007412_cerebellum	12.53 RPM	0.00 RPM
SRP007412_heart	3.91 RPM	0.00 RPM
SRP007412_kidney	13.33 RPM	0.00 RPM
SRP007412_liver	7.12 RPM	0.00 RPM
SRP007412_testis	15.64 RPM	0.00 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_1368 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1368 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_75
Pan troglodytes	retro_ptro_1278
Pongo abelii	retro_pabe_1581
Callithrix jacchus	retro_cjac_1147
Oryctolagus cuniculus	retro_ocun_1508
Rattus norvegicus	retro_rnor_1361
Canis familiaris	retro_cfam_1866
Equus caballus	retro_ecab_991

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000026660	1 retrocopy	retro_cpor_1434,
Equus caballus	ENSECAG00000018625	1 retrocopy	retro_ecab_991,
Gorilla gorilla	ENSGGOG00000025604	1 retrocopy	retro_ggor_1368 ,
Loxodonta africana	ENSLAFG00000026457	2 retrocopies	retro_lafr_214, retro_lafr_826,
Macropus eugenii	ENSMEUG00000015250	2 retrocopies	retro_meug_1196, retro_meug_205,
Myotis lucifugus	ENSMLUG00000024811	3 retrocopies	retro_mluc_1161, retro_mluc_1344, retro_mluc_673,
Monodelphis domestica	ENSMODG00000004273	2 retrocopies	retro_mdom_1444, retro_mdom_154,
Mus musculus	ENSMUSG00000031242	1 retrocopy	retro_mmus_1735,
Ochotona princeps	ENSOPRG00000018556	1 retrocopy	retro_opri_577,
Pongo abelii	ENSPPYG00000020505	1 retrocopy	retro_pabe_1581,
Pteropus vampyrus	ENSPVAG00000001416	2 retrocopies	retro_pvam_208, retro_pvam_59,
Rattus norvegicus	ENSRNOG00000002323	2 retrocopies	retro_rnor_1361, retro_rnor_623,
Sarcophilus harrisii	ENSSHAG00000016903	2 retrocopies	retro_shar_776, retro_shar_778,
Tarsius syrichta	ENSTSYG00000011727	1 retrocopy	retro_tsyr_1611,
Tursiops truncatus	ENSTTRG00000008066	2 retrocopies	retro_ttru_1002, retro_ttru_235,
Vicugna pacos	ENSVPAG00000000854	2 retrocopies	retro_vpac_112, retro_vpac_422,