RetrogeneDB ID: retro_pabe_2227

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:85376516..85377002(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSPPYG00000005090
• Aliases: None
• Description: transmembrane emp24 domain trafficking protein 2 [Source:HGNC Symbol;Acc:16996]

Sequence

>retro_pabe_2227
GTCACCTCAGGCACCAAGATGGGCCTCCTCTTCGAAGGTGGCTTCCTGGGCATCAACGTGGAGATGACAGGACCTAAGAA
TAAAAGGATTTATAAAGGAGACAAAGAATCCAGTGGGAAATACACATTTTCTGCTCACATGGATAGAACACATAAATTTT
GTTTTAGTAACTGAGTGTCCACCATGACTCCAAAGATAGTGATATTCACCATTGATATTGGGGAGGCTCCAAAAGGAGAA
GACATGGAAACAGAAGCTCACCAGAACAAACTAGAAGAAATGATCAGTGAGCTGGCTGTGGCCATGACAGCTGTACAGCG
CGAAGATGAATACATGAAAGTCTGGGAGAGGATACACAGAACCATTAGTGACAACACAAACAGCCCAGTGGTCCTTCGGT
GCTTCTTTGAAGCTCTTGTTCTAATTGCCATGACATTGGGACACATCTACTACCTGAAGAGATTTTTTGAAGTCCAGAGG
GTTGTT

Alignment

ORF - retro_pabe_2227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.21 %
• Parental protein coverage: 82.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGIYKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIV
          VTSGTKMGL.F...EGGFL.I.VE.TGP.NK.IYKGD.ESSGKYTF.AHMD.T.KFCFSN..STMTPKIV
Retrocopy VTSGTKMGLLF---EGGFLGINVEMTGPKNKRIYKGDKESSGKYTFSAHMDRTHKFCFSN*VSTMTPKIV

Parental  MFTIDIGEAPKGQDMETEAHQNKLEEMINELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFFE
          .FTIDIGEAPKG.DMETEAHQNKLEEMI.ELAVAMTAV..E.EYM.V.ERIHR.I.DNTNS.VVL..FFE
Retrocopy IFTIDIGEAPKGEDMETEAHQNKLEEMISELAVAMTAVQREDEYMKVWERIHRTISDNTNSPVVLRCFFE

Parental  ALVLVAMTLGQIYYLKRFFEVRRVV
          ALVL.AMTLG.IYYLKRFFEV.RVV
Retrocopy ALVLIAMTLGHIYYLKRFFEVQRVV

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	43.73 RPM
SRP007412_cerebellum	0.00 RPM	43.05 RPM
SRP007412_heart	0.00 RPM	45.58 RPM
SRP007412_kidney	0.00 RPM	63.44 RPM
SRP007412_liver	0.00 RPM	140.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2227 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2227 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2793
Gorilla gorilla	retro_ggor_1943
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,