RetrogeneDB ID: retro_ptro_283

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:27693313..27693854(-)
• Located in intron of: None

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_283
ATGGACGATACCCTGTTCCAGTTGAAATTTATGGTGAAGCAGCTGGAGAAACCACACAAGAAGGCAGAAAAGCACTCCTA
CGCCAACCAGGCCAAAGTGAAGAAGTCCCTTCAGCAGAAAAATGTAGAGTGCACCCGTGTGTACGCCAAGAACACCATCT
GCAAGGAGAACAGCAGCGTGAACTGGCTCTACATGGCATCCGCCTGGACACAGTGGCCCCAGAGATGCAGACAGCTGTGA
CCATGAAGGTGGTAACCAAGAACATGGTGTAGGTAACCAAAGCCCCAGACAAGGCCTGAACACCACGGACCTGCAGAAGG
CCTCTGCAGCGATGGACAGGTTTGAGTAGCAAGTGCAAAACCTGGCCATGCACACGTTAGTGATGGAGGATTCCATGAGC
TCGGCCACCACACTGACCATGCCTCAGGAGCAGGTGGACAGACCCATTGTGCAGAGCGCCAAGGAGAATGGCCTGGAGGT
CCTAGACCAGCTCAGCCAGTTGCCCAAGGGTGCCTCTGCCGGGCGAGAGCTCCGTGTGAAG

Alignment

ORF - retro_ptro_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.22 %
• Parental protein coverage: 92.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALLQKNVECARVYAENAIRKKNEGVNWLRMAS-RV
          MDDTLFQLKF..KQLEK..KKAEK.S.A.QAKVKK.L.QKNVEC.RVYA.N.I.K.N..VNWL.MAS.R.
Retrocopy MDDTLFQLKFMVKQLEKPHKKAEKHSYANQAKVKKSLQQKNVECTRVYAKNTICKENSSVNWLYMAS<RL

Parental  DAVASKVQTAVTMKGVTKNMAQVTKALDKA-LSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATT
          D.VA...QTAVTMK.VTKNM..VTKA.DKA.L.T.DLQK.S..MDRFE.QVQNL..HT.VMEDSMSSATT
Retrocopy DTVAPEMQTAVTMKVVTKNMV*VTKAPDKA<LNTTDLQKASAAMDRFE*QVQNLAMHTLVMEDSMSSATT

Parental  LTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR
          LT.PQEQVD..I.Q.A.ENGLEVLDQLSQLP.GASA..E..V.
Retrocopy LTMPQEQVDRPIVQSAKENGLEVLDQLSQLPKGASAGRELRVK

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	63.19 RPM
SRP007412_cerebellum	0.00 RPM	23.66 RPM
SRP007412_heart	0.00 RPM	7.61 RPM
SRP007412_kidney	0.00 RPM	69.46 RPM
SRP007412_liver	0.00 RPM	52.24 RPM
SRP007412_testis	0.00 RPM	28.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_283 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_283 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_359
Pongo abelii	retro_pabe_344
Macaca mulatta	retro_mmul_476

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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,