RetrogeneDB ID: retro_hsap_359

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:28013365..28013903(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSG00000131165
• Aliases: CHMP1A, CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A
• Description: charged multivesicular body protein 1A [Source:HGNC Symbol;Acc:8740]

Sequence

>retro_hsap_359
GACAATACCCTGTTCCAGTTGAAATTTATGGTGAAGCAGCTGGAGAAACCAGACAAGAAGGCAGAAAAGCACTCCTACGC
CAACCAGGCCAAAGTGAAGAAGTCCCTTCAGCAGAAAAATGTAGAGTGCACCCGTGTGTACACCAAGAACACCATCTGCA
AGGAGAACAGCAGCGTGAACTGGCTCTACATGGCATCCGCCTGGACACAGTGGCCCCCGAGGTGCAGACAGCTGTGACCA
TGAAGGTGGTAACCAAGAACATGGTGTAGGTGACCAAAGCCCCAGACAAGGCCTGAACACCACGGACCTGCAGAAGGCCT
CTGCAGCGATGGACAGGTTTGAGTAGCAAGTGCAAAACCTGGCCATGCACACATTAGTGATGGAGGATTCCATGAGCTCG
GCCGCCACACTGACCATGCCTCAGGAGCAGGTGGACAGACCCATTGTGCAGAGCGCCAAGGAGAATGGCCTGGAGGTCCT
AGACCAGCTCAGCCAGTTGCCCAAGGGTGCCTCTGCCGGGCGAGAGCTCCGTGTGAAG

Alignment

ORF - retro_hsap_359 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 91.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALLQKNVECARVYAENAIRKKNEGVNWLRMAS-RVD
          D.TLFQLKF..KQLEK..KKAEK.S.A.QAKVKK.L.QKNVEC.RVY..N.I.K.N..VNWL.MAS.R.D
Retrocopy DNTLFQLKFMVKQLEKPDKKAEKHSYANQAKVKKSLQQKNVECTRVYTKNTICKENSSVNWLYMAS<RLD

Parental  AVASKVQTAVTMKGVTKNMAQVTKALDKA-LSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTL
          .VA..VQTAVTMK.VTKNM..VTKA.DKA.L.T.DLQK.S..MDRFE.QVQNL..HT.VMEDSMSSA.TL
Retrocopy TVAPEVQTAVTMKVVTKNMV*VTKAPDKA<LNTTDLQKASAAMDRFE*QVQNLAMHTLVMEDSMSSAATL

Parental  TTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVR
          T.PQEQVD..I.Q.A.ENGLEVLDQLSQLP.GASA..E..V.
Retrocopy TMPQEQVDRPIVQSAKENGLEVLDQLSQLPKGASAGRELRVK

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
bodymap2_adipose	0.00 RPM	43.71 RPM
bodymap2_adrenal	0.00 RPM	44.56 RPM
bodymap2_brain	0.00 RPM	19.27 RPM
bodymap2_breast	0.00 RPM	38.68 RPM
bodymap2_colon	0.00 RPM	32.64 RPM
bodymap2_heart	0.00 RPM	14.93 RPM
bodymap2_kidney	0.00 RPM	39.50 RPM
bodymap2_liver	0.00 RPM	16.43 RPM
bodymap2_lung	0.00 RPM	31.45 RPM
bodymap2_lymph_node	0.00 RPM	34.85 RPM
bodymap2_ovary	0.00 RPM	46.77 RPM
bodymap2_prostate	0.00 RPM	43.79 RPM
bodymap2_skeletal_muscle	0.00 RPM	32.25 RPM
bodymap2_testis	0.02 RPM	47.21 RPM
bodymap2_thyroid	0.00 RPM	46.76 RPM
bodymap2_white_blood_cells	0.00 RPM	60.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_359 was not detected

EST

No EST(s) were mapped for retro_hsap_359 retrocopy.

TSS

No TSS is located nearby retro_hsap_359 retrocopy 5' end.

Lab

retro_hsap_359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_359 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_283
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).