RetrogeneDB ID: retro_hsap_4716

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:75443049..75443493(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000237252
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMADHC
• Ensembl ID: ENSG00000168288
• Aliases: MMADHC, C2orf25, CL25022, cblD
• Description: methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:HGNC Symbol;Acc:25221]

Sequence

>retro_hsap_4716
AGAGTAGAGTGTGCAACCCAAGCATGTCCAGAATTGCTGTGAAGAGATTTTGAATCATTATTTCCAGAAGTGGCTAATAG
CAAACTAATGATTCTGACTATAACACCACAAAACCAAGAATGATATGATAGTTTGACATGAAGAAGTAGAAATTGAAAGA
GAAACGCTCTTGGAAAAGTTTATCAATAGTGCTAAAGAAATTTGCTATGCACTTCAAGCTGAGGATAGTGGGCTGAATTA
ATTGGTTTGGCATTTTTTGGACCATGTATAAACAACCCTCTTTTTAAAACAGATGAAAGCTACTAACATTTAGGATTATC
TGTTGATGATCTTGGATAATGTGAAGCGATTTATCATAGTCTCTGGGGCACCGATGTATTTGTCGGAAGTATGTTCACTA
ATGCAACACCAGACAGCCATATTATAGAGAAATTAAGGGGAAAT

Alignment

ORF - retro_hsap_4716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 51.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVECAIQTCPELLRKDFESLFPEVANGKLMILTVT-QKTKNDMTVWSEEVEIEREVLLEKFINGAKEICY
          RVECA.Q.CPELL..DFESLFPEVAN.KLMILT.T..KTKNDM.V..EEVEIERE.LLEKFIN.AKEICY
Retrocopy RVECATQACPELL*RDFESLFPEVANSKLMILTIT>HKTKNDMIV*HEEVEIERETLLEKFINSAKEICY

Parental  ALRAE-GYWADFIDPSSGLAFFGPYTNNTLFETDERYRHLGFSVDDLGCCKVIRHSLWGTHVVVGSIFTN
          AL.AE.G.WA..I....GLAFFGP..NN.LF.TDE.Y.HLG.SVDDLG.C..I.HSLWGT.V.VGS.FTN
Retrocopy ALQAE<G*WAELI----GLAFFGPCINNPLFKTDESY*HLGLSVDDLG*CEAIYHSLWGTDVFVGSMFTN

Parental  ATPDSHIMKKLSGN
          ATPDSHI..KL.GN
Retrocopy ATPDSHIIEKLRGN

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	60.65 RPM
bodymap2_adrenal	0.00 RPM	60.36 RPM
bodymap2_brain	0.00 RPM	45.68 RPM
bodymap2_breast	0.00 RPM	81.65 RPM
bodymap2_colon	0.00 RPM	86.97 RPM
bodymap2_heart	0.00 RPM	83.00 RPM
bodymap2_kidney	0.00 RPM	85.95 RPM
bodymap2_liver	0.00 RPM	85.68 RPM
bodymap2_lung	0.00 RPM	55.47 RPM
bodymap2_lymph_node	0.00 RPM	65.40 RPM
bodymap2_ovary	0.00 RPM	65.83 RPM
bodymap2_prostate	0.00 RPM	95.16 RPM
bodymap2_skeletal_muscle	0.00 RPM	87.94 RPM
bodymap2_testis	0.00 RPM	86.27 RPM
bodymap2_thyroid	0.00 RPM	83.65 RPM
bodymap2_white_blood_cells	0.00 RPM	82.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4716 was not detected

EST

No EST(s) were mapped for retro_hsap_4716 retrocopy.

TSS

No TSS is located nearby retro_hsap_4716 retrocopy 5' end.

Lab

retro_hsap_4716 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4716 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003086	2 retrocopies	retro_cjac_4082, retro_cjac_4101,
Cavia porcellus	ENSCPOG00000007690	1 retrocopy	retro_cpor_30,
Homo sapiens	ENSG00000168288	2 retrocopies	retro_hsap_4716 , retro_hsap_865,
Gorilla gorilla	ENSGGOG00000027348	1 retrocopy	retro_ggor_704,
Macaca mulatta	ENSMMUG00000005633	1 retrocopy	retro_mmul_1058,
Monodelphis domestica	ENSMODG00000003566	2 retrocopies	retro_mdom_1749, retro_mdom_620,
Mustela putorius furo	ENSMPUG00000000323	1 retrocopy	retro_mputfur_1253,
Nomascus leucogenys	ENSNLEG00000010795	2 retrocopies	retro_nleu_1988, retro_nleu_426,
Otolemur garnettii	ENSOGAG00000034385	4 retrocopies	retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes	ENSPTRG00000012525	1 retrocopy	retro_ptro_599,
Ictidomys tridecemlineatus	ENSSTOG00000021576	1 retrocopy	retro_itri_1809,
Tarsius syrichta	ENSTSYG00000009075	1 retrocopy	retro_tsyr_1690,

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	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 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	0.06 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 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).