RetrogeneDB ID: retro_pabe_1919

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22_random:2844824..2845258(-)
• 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_1919
GTGCTCCTGGCCACTCTCCTGGCCCGGTCTCAGGCTACTTTATTAGCTTCGACCTGCATGCCGAGAAGTGCTTCTTTGAG
CGGGTCACCTCGGGCACCAAGATGGGCCTCATGTCTGAAATGGCGGAGGGCGACTTCCTATACATCGACGTGGAGATTAC
AGAACCAGATAATAAAGGGATTTACAAAGGAGACCGAGAATCCAGTGGGAAAAACACATTTGCTCCTCACATGGTTGGAA
CTTAGAAATTTTGTTTTAGTAACCGGATGTCTACCATCACTCCAAAAATAGTGAGGTTCACCATTGATATTGGAGAGGCT
CCAAAAGGACAAGACATGGAAAAAGGAGCTCACCACAACAAGCTAGAAGAAATGATCAGTGAACTAGCAGTGGCGATCAC
AGCTGTAAAGCACAAACAGGAATACATGGAAATT

Alignment

ORF - retro_pabe_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.19 %
• Parental protein coverage: 72.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLLAALLAT-VSGYFVSIDAHAEECFFERVTSGTKMGLIFEVAEGGFLDIDVEITGPDNKGIYKGDRESS
          VLLA.LLA..VSGYF.S.D.HAE.CFFERVTSGTKMGL..E.AEG.FL.IDVEIT.PDNKGIYKGDRESS
Retrocopy VLLATLLAR<VSGYFISFDLHAEKCFFERVTSGTKMGLMSEMAEGDFLYIDVEITEPDNKGIYKGDRESS

Parental  GKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDIGEAPKGQDMETEAHQNKLEEMINELAVAMTAVKHE
          GK.TFA.HM.GT.KFCFSNRMST.TPKIV.FTIDIGEAPKGQDME..AH.NKLEEMI.ELAVA.TAVKH.
Retrocopy GKNTFAPHMVGT*KFCFSNRMSTITPKIVRFTIDIGEAPKGQDMEKGAHHNKLEEMISELAVAITAVKHK

Parental  QEYMEV
          QEYME.
Retrocopy QEYMEI

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	0.44 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	0.03 RPM	140.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1919 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1919 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1919 has 0 orthologous retrocopies within eutheria group .

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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,