RetrogeneDB ID: retro_cjac_1848

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:137784220..137785056(+)
• Located in intron of: ENSCJAG00000016093

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007018
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F6YJ68]

Sequence

>retro_cjac_1848
GTCCTAATGTAACTGTAAGACTATACCCTTCCCCTCCTGAAAGATGTCATTGCAACAGAAGAGGTTTCCTTCAAAAACCT
GGATGTGGTCTTTCTTGTGGCCTCCATGCAAAGAAGGGAAGGCATGGAGAGAAAAGATTTACTGAAAGCAAATGTGAAAA
TCTTCAAATCCCAGGGTGCAGCCTTGGAGAAGTACGACAAAAAGTCAGGTAAGGTTATTGTTGTGGGTAATCCAGCCAAT
ACCAACTGCCTGACTGCCTCCAGTCAGCTCCATCCATGCCCAAGGAAAACTTCAGTTCAGTTGCTTGACTTGTTTGGATC
ACAACCGAGCTAAAGCTCAAATTGCTCTTCAACTTGATGTGACTGCTAATGATGTAATAAATGTCATTATCCGGGGAAAC
CATTTCTTGACTCAGTATCCAGATGTCAACCATGCCAAAGTAAAATTGCAAGGAAAGGAAGTTGTGTTTATGAAGTTCTG
AAAGATGACAGCAGGCTCTAGGAGAATTTGTCACGACTATGCAGCAGCATGGCACTGCTACCATCAAGGCTTGAAAACTA
TCCAGAGCAATGTCTGCTGCAAAAGCCATCTATGACCACATCAGGGACATGTTTGTGTCAGAGGGAGAGTTTGTGTCCAT
GGGTGTTATCTCTGATGGCAACTCCTATGGTATTCCTGATGATCTACTCTGCTCATTCCCTGTCGTAATCAAGAATAAGA
CCTAGAAGTTTGTTGAAGGTCTCCCTATTAAAGATTTTTCATGTGAGAAGATAGATCTTACTGCAAAGGAACTGACAGAA
GAAAAAGAAACTGCTTTTGAATTTCTTTCCTCTGCC

Alignment

ORF - retro_cjac_1848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.44 %
• Parental protein coverage: 84.34 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLMELQDCALPLLKDVIATDKEEVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAALDKYAKK
          VLM.L.D..LPLLKDVIAT..EEV.FK.LDV..LV.SM.RREGMERKDLLKANVKIFKSQGAAL.KY.KK
Retrocopy VLM*L*DYTLPLLKDVIAT--EEVSFKNLDVVFLVASMQRREGMERKDLLKANVKIFKSQGAALEKYDKK

Parental  SVK-VIV-VGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTANDVKNVIIWGNHSST
          S.K...V.V..P..T..L....S.....K..FSCLT.LDHNRAKAQIAL.L.VTANDV.NVII.GNH..T
Retrocopy SGKVIVV>VIQPIPTA*LPPVSSIHAQGKLQFSCLTCLDHNRAKAQIALQLDVTANDVINVIIRGNHFLT

Parental  QYPDVNHAKVKLQGKEVG-VYEALKDDNWL-KGEFVTTVQQRGAAVIKARKLSSAMSAAK-ICDHVRDIW
          QYPDVNHAKVKLQGKEV..VYE.LKDD..L..GEFVTT.QQ.G.A.IKA.KLS.AMSAAK.I.DH.RD..
Retrocopy QYPDVNHAKVKLQGKEVV<VYEVLKDDSRL<LGEFVTTMQQHGTATIKA*KLSRAMSAAKAIYDHIRDM-

Parental  FTPEGEFVSMGVISDGNSYGVPDDLLYSFPVVIKNKTWKFVEGLPVNDFSREKMDLTAKELTEEKETAFE
          F..EGEFVSMGVISDGNSYG.PDDLL.SFPVVIKNKT.KFVEGLP..DFS.EK.DLTAKELTEEKETAFE
Retrocopy FVSEGEFVSMGVISDGNSYGIPDDLLCSFPVVIKNKT*KFVEGLPIKDFSCEKIDLTAKELTEEKETAFE

Parental  FLSSA
          FLSSA
Retrocopy FLSSA

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	0.80 RPM	51.43 RPM
SRP051959_heart	0.40 RPM	198.01 RPM
SRP051959_kidney	0.60 RPM	89.12 RPM
SRP051959_liver	0.24 RPM	68.53 RPM
SRP051959_lung	0.75 RPM	21.81 RPM
SRP051959_lymph_node	1.10 RPM	26.09 RPM
SRP051959_skeletal_muscle	0.28 RPM	157.47 RPM
SRP051959_spleen	0.63 RPM	30.57 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1848 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1848 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848 , retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,