RetrogeneDB ID: retro_cjac_4101

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:92593702..92594590(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003345
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_4101
ATGGCCAATGTGCTTTGCAACAAAGTCAGACTGGTTTCCTATCTCCCAGGATTTTGCTCTTTAGTTAAAAGGGTTGTCAA
TCCCAGAGCCTTTTCAACTGCAGGATCGTCAGGTTCAGACGAGTCTCATGTGGCCACTGCAACCCCAGATATATGCTCTC
GAACAGTGTGGCCTGATGAAACTATGGGACCATTTGGACCTCAAGATCAGAGGTTCCAGTTTCCTGGGAACATAGGTTTT
GATTGTCACCTCAATGGTACTGCTTCACAGAAGAAAAGCCTGGTTCATAAAACTTTGCCTGGTGTTCTAGCAGAACCTTT
ATCAAGTGAAAGACATGAGTTTGTGATGGCACAGTACATGAATGAATTTCAGGGTAATGATGCACCTGTTGAACAAGAAA
TTAACAGTGCAGAAACTCACTTTGAAAGTGCCAGAGTAGAGTGCACAATACAAACATGTCCAGAATTGCTGCGAAAAGAT
TTTGAATCACTGTTTCCAGAAGTAGCTAACAGCAAACTAATGATTCTGACTGTAACACAAAAAACTAAGAACGATATGAC
TGTTTGGAGTGAAGAAGTAGAAATTGAAAGAGAAGTGCTCTTAGAAAAGTTCATCAATGTTGCTAAGGAAATTTGTTTTG
CTCTTCGAGCTGAGGGCTATTGGGCTGACTTTATTGACCCATCATCTGGTTTGGCATTTTTTGGACCATATACAAACAAC
ACTCTTTTTGAAACCGATGAACGTTACCGACATTTAGGATTCTCTGTTGATGACCTTGGATGCTGTAACGTGATTCGTCA
CAGTCTTTGGGGTACCCATGTATTTGTGAGAAGTATCTTCACTAATGCAACACCAGAGAGCCATATTATGAAGAAATTGA
GTGGAAAT

Alignment

ORF - retro_cjac_4101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANVLCNKVRLVSYLPGFCSLVKRVVNPRAFSTAGSSGSDESHVATATPDICSRTVWPDETMGPFGPQDQ
          MANVLCNKVRLVSYLPGFCSLVKRVVNPRAFSTAGSSGSDESHVATATPDICSRTVWPDETMGPFGPQDQ
Retrocopy MANVLCNKVRLVSYLPGFCSLVKRVVNPRAFSTAGSSGSDESHVATATPDICSRTVWPDETMGPFGPQDQ

Parental  RFQLPGNIGFDCHLNGTASQKKSLVHKTLPDVLGEPLSSERHEFVMAQYVNEFQGNDAPVEQEINSAETY
          RFQ.PGNIGFDCHLNGTASQKKSLVHKTLP.VL.EPLSSERHEFVMAQY.NEFQGNDAPVEQEINSAET.
Retrocopy RFQFPGNIGFDCHLNGTASQKKSLVHKTLPGVLAEPLSSERHEFVMAQYMNEFQGNDAPVEQEINSAETH

Parental  FESARVECAIQTCPELLRKDFESLFPEVANSKLMILTVTQKTKNDMTVWSEEVEIEREVLLEKFINGAKE
          FESARVEC.IQTCPELLRKDFESLFPEVANSKLMILTVTQKTKNDMTVWSEEVEIEREVLLEKFIN.AKE
Retrocopy FESARVECTIQTCPELLRKDFESLFPEVANSKLMILTVTQKTKNDMTVWSEEVEIEREVLLEKFINVAKE

Parental  ICFALRAEGYWADFIDPSSGLAFFGPYTNNTLFETDERYRHLGFSVDDLGCCKVIRHSLWGTHVFVGSIF
          ICFALRAEGYWADFIDPSSGLAFFGPYTNNTLFETDERYRHLGFSVDDLGCC.VIRHSLWGTHVFV.SIF
Retrocopy ICFALRAEGYWADFIDPSSGLAFFGPYTNNTLFETDERYRHLGFSVDDLGCCNVIRHSLWGTHVFVRSIF

Parental  TNATPESHIMKKLSGN
          TNATPESHIMKKLSGN
Retrocopy TNATPESHIMKKLSGN

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	2.35 RPM	25.98 RPM
SRP051959_heart	2.37 RPM	23.89 RPM
SRP051959_kidney	3.15 RPM	30.48 RPM
SRP051959_liver	5.29 RPM	42.52 RPM
SRP051959_lung	1.95 RPM	14.45 RPM
SRP051959_lymph_node	1.44 RPM	11.57 RPM
SRP051959_skeletal_muscle	6.51 RPM	55.29 RPM
SRP051959_spleen	2.00 RPM	16.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4101 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4101 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,