RetrogeneDB ID: retro_ggor_1943

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:62282796..62283282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSGGOG00000028536
• Aliases: None
• Description: None

Sequence

>retro_ggor_1943
GTCACCTCAGGCACCAAGATGGGCCTCATCTTCGAAGGTGGCTTCCTGGGCATCAACGTGGAGATTACAGGACCTAAGAA
TAAAAGGATTTATAAAGGAGACAAAGAATCCAGTGGGAAATACACATTTTCTGCTCACATGGATGGAACAAATAAATTTT
GTTTTAGTGACGGAGTGTCCACCATGACTCCAAAGATAGTGATATTCACCACTGATATTGGGGAGGCTACAAAAGGAGAA
GACATGGAAACAGAAGCTCACCAGAACAAACTAGAAGAAATGATCAGTGAGCTGGCTGTGGCCATGACAGCTGTACAGCA
CAAAGAGGAATACACGAAAATCTGGGAGAGGATACACAGAGCCATTAGTGACAACACAAACAGCCCAGTGGTCCTTCGGT
CCTTCTTTGAAACTCTTGTTCTAAATGCTATGATATTGGGACACATCTACTACCTGAAGAGATTTTTTGAAGTCCAGAGG
GTTGTT

Alignment

ORF - retro_ggor_1943 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.47 %
• Parental protein coverage: 82.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGIYKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIV
          VTSGTKMGLIF...EGGFL.I.VEITGP.NK.IYKGD.ESSGKYTF.AHMDGT.KFCFS...STMTPKIV
Retrocopy VTSGTKMGLIF---EGGFLGINVEITGPKNKRIYKGDKESSGKYTFSAHMDGTNKFCFSDGVSTMTPKIV

Parental  MFTIDIGEAPKGQDMETEGEMNIQKIYITFQELIVIVFNVGHLQKNKTLHEFLSSTVNDNTNSRVVLWSF
          .FT.DIGEA.KG.DMETE...N..K......EL.V....V.H........E.......DNTNS.VVL.SF
Retrocopy IFTTDIGEATKGEDMETEAHQN--KLEEMISELAVAMTAVQHKEEYTKIWERIHRAISDNTNSPVVLRSF

Parental  FEALVLVAMTLGQIYYLKRFFEVRRVV
          FE.LVL.AM.LG.IYYLKRFFEV.RVV
Retrocopy FETLVLNAMILGHIYYLKRFFEVQRVV

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	1.58 RPM	36.06 RPM
SRP007412_cerebellum	0.95 RPM	21.12 RPM
SRP007412_heart	0.19 RPM	9.94 RPM
SRP007412_kidney	3.35 RPM	31.24 RPM
SRP007412_liver	3.14 RPM	43.60 RPM
SRP007412_testis	4.04 RPM	48.07 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_1943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1943 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2793
Pongo abelii	retro_pabe_2227
Macaca mulatta	retro_mmul_1439
Callithrix jacchus	retro_cjac_1392

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015262	2 retrocopies	retro_amel_1923, retro_amel_337,
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus	ENSCJAG00000020466	1 retrocopy	retro_cjac_1392,
Echinops telfairi	ENSETEG00000000556	2 retrocopies	retro_etel_2109, retro_etel_2154,
Homo sapiens	ENSG00000086598	1 retrocopy	retro_hsap_2793,
Gorilla gorilla	ENSGGOG00000028536	1 retrocopy	retro_ggor_1943 ,
Macaca mulatta	ENSMMUG00000031491	2 retrocopies	retro_mmul_1439, retro_mmul_613,
Mustela putorius furo	ENSMPUG00000001598	1 retrocopy	retro_mputfur_1241,
Mus musculus	ENSMUSG00000029390	2 retrocopies	retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys	ENSNLEG00000001652	2 retrocopies	retro_nleu_2454, retro_nleu_2794,
Otolemur garnettii	ENSOGAG00000009192	1 retrocopy	retro_ogar_2548,
Pongo abelii	ENSPPYG00000005090	3 retrocopies	retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,