RetrogeneDB ID: retro_ptro_2398

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:147683362..147683909(+)
• Located in intron of: ENSPTRG00000018684

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUNDC2
• Ensembl ID: ENSPTRG00000041852
• Aliases: None
• Description: Pan troglodytes FUN14 domain containing 2 (FUNDC2), mRNA. [Source:RefSeq mRNA;Acc:NM_001251911]

Sequence

>retro_ptro_2398
CGTGCCAAAAGCCACCTGGTGTGGCAACTGCACACCACTCTGCATCCTACAGCGTGGATCCTCTGCATGTGCTTTTGGGA
GATGAGCTCACTGAAATGGCCATGTCCAGTCAAGGACACTTTGAGGGAAATTTTGAGTCTCTGGATCTTGCAGAATTTGC
TCAAAATCAGCCATGGGGGAATAAGATGTTTGGACAGGAATCTGGATCTCTGGCTAAAAAGTATCCTGTGGCAACCCAGC
TGTTAATTGGAAGCTTCACTAGATGATGCATGGAGTTCATATTCCAAAAGGTTGAAAATTGGCTGCAACAGCTGTGGGGG
GTGAATTTTTTCTCCTTCAGCTTGCAAGTCATACTGAGTACATCAAAGATGACTGGCAACAACTGGAGGAGGACATGAAG
AAAGCAAAAGAACAGCTGAAGATCCATAAAAGCAATCAGATACCTACTGAGGTCAAGAGCAAAGCTGAGGAGGTGGTGTC
ATTTGTGAAGAAGAATGTTCTAATGACTGGGGAAATTTTCAGAGGTCTTCTGCTTGGCATGGCATCA

Alignment

ORF - retro_ptro_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 96.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RAGSQVV-ATTARHSAAYRADPLRVASRDKLTEMAASSQGNFEGNFESLDLAEFAKKQPWWRKLFGQESG
          RA.S..V...TA.HSA.Y..DPL.V...D.LTEMA.SSQG.FEGNFESLDLAEFA..QPW..K.FGQESG
Retrocopy RAKSHLV<VATAHHSASYSVDPLHVLLGDELTEMAMSSQGHFEGNFESLDLAEFAQNQPWGNKMFGQESG

Parental  PSAEKYSVATQLFIGGVTGWCTGFIFQKVG-KLAATAVGGGFFLLQLANHTGYIKVDWQRVEKDMKKAKE
          ..A.KY.VATQL.IG..T..C..FIFQKV..KLAATAVGG.FFLLQLA.HT.YIK.DWQ..E.DMKKAKE
Retrocopy SLAKKYPVATQLLIGSFTR*CMEFIFQKVE<KLAATAVGGEFFLLQLASHTEYIKDDWQQLEEDMKKAKE

Parental  QLKIRKSNQIPTEVRSKAEEVVSFVKKNVLVTGGFFGGFLLGMAS
          QLKI.KSNQIPTEV.SKAEEVVSFVKKNVL.TG..F.G.LLGMAS
Retrocopy QLKIHKSNQIPTEVKSKAEEVVSFVKKNVLMTGEIFRGLLLGMAS

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	0.05 RPM	28.81 RPM
SRP007412_cerebellum	0.11 RPM	26.78 RPM
SRP007412_heart	0.03 RPM	48.38 RPM
SRP007412_kidney	0.00 RPM	33.24 RPM
SRP007412_liver	0.00 RPM	9.43 RPM
SRP007412_testis	0.00 RPM	31.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2398 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2398 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3530
Pongo abelii	retro_pabe_2916
Callithrix jacchus	retro_cjac_2387

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016977	1 retrocopy	retro_btau_292,
Choloepus hoffmanni	ENSCHOG00000004306	11 retrocopies	retro_chof_1501, retro_chof_161, retro_chof_1640, retro_chof_1674, retro_chof_2087, retro_chof_2351, retro_chof_2355, retro_chof_2396, retro_chof_2491, retro_chof_2519, retro_chof_580,
Callithrix jacchus	ENSCJAG00000004287	3 retrocopies	retro_cjac_1977, retro_cjac_2387, retro_cjac_651,
Dipodomys ordii	ENSDORG00000013156	1 retrocopy	retro_dord_597,
Echinops telfairi	ENSETEG00000013817	2 retrocopies	retro_etel_1724, retro_etel_435,
Homo sapiens	ENSG00000165775	3 retrocopies	retro_hsap_2122, retro_hsap_2560, retro_hsap_3530,
Loxodonta africana	ENSLAFG00000015289	1 retrocopy	retro_lafr_2,
Myotis lucifugus	ENSMLUG00000007776	1 retrocopy	retro_mluc_219,
Macaca mulatta	ENSMMUG00000010248	1 retrocopy	retro_mmul_78,
Monodelphis domestica	ENSMODG00000016484	1 retrocopy	retro_mdom_1736,
Mus musculus	ENSMUSG00000031198	2 retrocopies	retro_mmus_2241, retro_mmus_2242,
Nomascus leucogenys	ENSNLEG00000014443	5 retrocopies	retro_nleu_1512, retro_nleu_1662, retro_nleu_1958, retro_nleu_2386, retro_nleu_494,
Otolemur garnettii	ENSOGAG00000033461	3 retrocopies	retro_ogar_1146, retro_ogar_132, retro_ogar_762,
Pongo abelii	ENSPPYG00000020897	4 retrocopies	retro_pabe_1884, retro_pabe_2646, retro_pabe_2916, retro_pabe_49,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Pan troglodytes	ENSPTRG00000041852	4 retrocopies	retro_ptro_1490, retro_ptro_1553, retro_ptro_2254, retro_ptro_2398 ,
Pteropus vampyrus	ENSPVAG00000013552	1 retrocopy	retro_pvam_210,
Rattus norvegicus	ENSRNOG00000024066	2 retrocopies	retro_rnor_1648, retro_rnor_2870,
Sus scrofa	ENSSSCG00000012817	1 retrocopy	retro_sscr_274,
Ictidomys tridecemlineatus	ENSSTOG00000007801	2 retrocopies	retro_itri_1157, retro_itri_1399,