RetrogeneDB ID: retro_cjac_4082

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:67720973..67721428(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMADHC
• Ensembl ID: ENSCJAG00000003086
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria [Source:HGNC Symbol;Acc:25221]

Sequence

>retro_cjac_4082
AGAGTAGAGTATGCAATCCAAGTGTGTCAAAAATTGCTATGAAGAGATTTTGAATTATTATTTCCAGAAGTGGCTAATAG
CAAACTAATGATTCTGACTATAATACTACAAAATCAAGAATGATATGATAGTTTGACAAGAAGAAGTAAAAATTGAAAAA
GAAATGCTCTTTAAAAAGTTTATCAATTGTGCTAAGGAAATTTGCTATGCACTTCAAGCTGAGTGATATTGGGCTGACTT
TATAGACCCATCATCTGGTTTGGCATTTTTTGGACCATGTATAAACAGCACTCTTTTTAAAACAGGTAAAAACTAGTACA
TTTAGGGTTATTTGTTGATTATCTTGGATGACGTAAAGCTATTTATCATGGTCTCTGTGCACCCATATAGTTGTATGAAG
TATGTTCACTAATGCAACACCAGCCAGCCATATTATAGAGAAATTAAGGGGAAAT

Alignment

ORF - retro_cjac_4082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.81 %
• Parental protein coverage: 51.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RVECAIQTCPELLRKDFESLFPEVANSKLMILTVT-QKTKNDMTVWSEEVEIEREVLLEKFINGAKEICF
          RVE.AIQ.C..LL..DFE.LFPEVANSKLMILT....K.KNDM.V..EEV.IE.E.L..KFIN.AKEIC.
Retrocopy RVEYAIQVCQKLL*RDFELLFPEVANSKLMILTII>YKIKNDMIV*QEEVKIEKEMLFKKFINCAKEICY

Parental  ALRAEGYWADFIDPSSGLAFFGPYTNNTLFETDE-RYRHLGFSVDDLGCCKVIRHSLWG-THVFVGSIFT
          AL.AE.YWADFIDPSSGLAFFGP..N.TLF.T......HLG..VD.LG..K.I.H.L...TH..V.S.FT
Retrocopy ALQAE*YWADFIDPSSGLAFFGPCINSTLFKTGK<KLVHLGLFVDYLG*RKAIYHGLCA<THIVV*SMFT

Parental  NATPESHIMKKLSGN
          NATP.SHI..KL.GN
Retrocopy NATPASHIIEKLRGN

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
SRP051959_colon	0.02 RPM	25.98 RPM
SRP051959_heart	0.02 RPM	23.89 RPM
SRP051959_kidney	0.00 RPM	30.48 RPM
SRP051959_liver	0.00 RPM	42.52 RPM
SRP051959_lung	0.07 RPM	14.45 RPM
SRP051959_lymph_node	0.00 RPM	11.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	55.29 RPM
SRP051959_spleen	0.04 RPM	16.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4082 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4082 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,