RetrogeneDB ID: retro_ptro_1278

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:4709738..4710320(-)
• Located in intron of: ENSPTRG00000009871

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSPTRG00000008483
• Aliases: None
• Description: charged multivesicular body protein 1A [Source:HGNC Symbol;Acc:8740]

Sequence

>retro_ptro_1278
ATGGAGAAACACCTGTTCAACCTGAAGTTCGCGGCCAAAGAACTGAGTAGGAGTGCCAAAAAATGCGATAAGGAGGAAAA
GGCCGAAAAGGCCAAAATTAAAAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATACACGCCGAAAATGCCATCC
GCCAGAAGAACCAGGCGGTGAATTTCTTGAGAATGAGTGCGCGAGTCGATGCAGTGGCTGCCAGGGTCCAGACGGCGGTG
ACCATGGGCAAGGTGACCAAGTCGATGGCTGGTGTGGTTAAGTCGATGGATGCGACATTGAAGACCATGAATCTGGAGAA
GATTTCTGCTTTGATGGACAAATTCGAGCACCAGTTTGAGACTCTGGACGTCCAGACGCAGCAAATGGAAGACACGATGA
GCAGCACGACGACGCTCACCACTCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGATGAGGCGGGCCTCGAC
CTCAACATGGAGCTGCCGCAGGGCCAGACCGGCTCCGTGGGCACGAGCGTGGCTTCGGCGGAGCAGGATGAACTGTCTCA
GAGACTGGCCCGCCTTCGGGAT

Alignment

ORF - retro_ptro_1278 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALLQKNVECARVYAENAIRKKNEGVNWLRMASRVD
          M...LF.LKF.AK.L...AKK..K..KAE.AK.KKA....N.E.AR..AENAIR.KN..VN.LRM..RVD
Retrocopy MEKHLFNLKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVD

Parental  AVASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLT
          AVA..VQTAVTM..VTK.MA.V.K..D..L.TM.L.K.S..MD.FE.Q...LDV.T..MED.MSS.TTLT
Retrocopy AVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLT

Parental  TPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          TPQ.QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
Retrocopy TPQNQVDMLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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	16.84 RPM	63.19 RPM
SRP007412_cerebellum	20.11 RPM	23.66 RPM
SRP007412_heart	15.45 RPM	7.61 RPM
SRP007412_kidney	26.15 RPM	69.46 RPM
SRP007412_liver	24.62 RPM	52.24 RPM
SRP007412_testis	11.07 RPM	28.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1278 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1278 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_75
Gorilla gorilla	retro_ggor_1368
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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278 , retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,