RetrogeneDB ID: retro_pabe_344

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:202652321..202652864(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSPPYG00000007667
• Aliases: CHMP1A, PCOLN3
• Description: Charged multivesicular body protein 1a [Source:UniProtKB/Swiss-Prot;Acc:Q5R605]

Sequence

>retro_pabe_344
ATGGACGATACCTTGTTCCAGTTGAAATTTATGGTGAAGCAGCTGGAGAAACCAGACAAGAAGGCAGAAAAGCACTGCTA
TGCCAACCAGGCCAAAGTGAAGAAGTCCCTTCAGCAGAAAAACGTAGAGTGCACCTGTGTGTACGCCAAGAACACCATCT
GCAAGGAGAACAGCAGCGTGAACTGGCTCTGCATGGCATCCGCCTGGACACAGTGGCCCCCGAGGTGCGGACAGCTGTGA
CCATGAAGGTGGTAACCAAGAACATGGTGTAGGTGACCAAAGCCCCAGACAAGGCCCTGAACACCACGGACCTGCAGAAG
GGCCTCTGCAGCGATGGACAGGTTCGAGTAGCAAGCGCAAAACCTGGCCGTGCACACGTTAGTGATGGAGGATTCCATGA
GCTCGGCCACCACACTGACTATGCCTCAGGAGCAGGTGGAGAGCCCCACTGTGCAGAGCGCCAAGGAGAATGGCCTGGAG
GTCCTAGACCAGCTCAGCCAGTTGCCCAAGGGTGCCTCTGCCAGGCGAGAGCTCCTTGTGAAG

Alignment

ORF - retro_pabe_344 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.58 %
• 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...A.QAKVKK.L.QKNVEC..VYA.N.I.K.N..VNWL.MAS.R.
Retrocopy MDDTLFQLKFMVKQLEKPDKKAEKHCYANQAKVKKSLQQKNVECTCVYAKNTICKENSSVNWLCMAS<RL

Parental  DAVASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQK-VSSVMDRFEQQVQNLDVHTSVMEDSMSSATT
          D.VA..V.TAVTMK.VTKNM..VTKA.DKAL.T.DLQK..S..MDRFE.Q.QNL.VHT.VMEDSMSSATT
Retrocopy DTVAPEVRTAVTMKVVTKNMV*VTKAPDKALNTTDLQK>ASAAMDRFE*QAQNLAVHTLVMEDSMSSATT

Parental  LTTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR
          LT.PQEQV.S...Q.A.ENGLEVLDQLSQLP.GASA..E..V.
Retrocopy LTMPQEQVESPTVQSAKENGLEVLDQLSQLPKGASARRELLVK

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	42.79 RPM
SRP007412_cerebellum	0.00 RPM	30.28 RPM
SRP007412_heart	0.00 RPM	12.19 RPM
SRP007412_kidney	0.00 RPM	63.91 RPM
SRP007412_liver	0.00 RPM	29.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_344 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_344 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_344 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_359
Pan troglodytes	retro_ptro_283
Macaca mulatta	retro_mmul_476

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 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 ,
Pongo abelii	ENSPPYG00000020505	1 retrocopy	retro_pabe_1581,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311,