RetrogeneDB ID: retro_cjac_2830

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:95253605..95254677(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011633
• Aliases: None
• Description: None

Sequence

>retro_cjac_2830
CTTCCCCACCCGGCGCGACGACAGCTCTTGGGAGGTCATCAAAGGCTGGGAGGTCACTGGGCCCAGCACAGCCAGCACCG
CACTCCCCGCAAGGGAGGTATCCGTCACAGCACTGCTTGAGTGTAGATGAAGTAAAAGCTTTGGCTTCTCTGATGACATA
CAAATGTGCAGTGGTTAATGTGCCGTTTGGGGGCGCTAACGCTGGTGTTGAGATCAATCCCAAGAACTACTATACTGATA
ATGAATTGGACAAGATCACAAGGAGGTTCACCATGGAGCTGGCAAAGAAGGGCTTTATTGGTCCTGGCATTGATGTCCCT
GCCCCAGACATGAACACAGGTGAGGGGGAGATGTCCTGGATCCCTGATATCTATGCCAGCACCATAGGCCACTGCAATAT
TAATGCACATGCCTGTGTTACTGGTAAACCCATCAGTCAAGGGGGCATCCACGGACGCATTTCTGCTACTGGCCATGGTG
TCTTCCATGGGGTTGAAAACTTCATCAGTGAAGCTTCTTACATGAGCATTTTAGGAATGACACCAGGATTTGGAGATAAA
ACATTTGTTGTTCAGGGATTTGGGTAATGTGGGCCTACACTCTATGATATTTGCATCGTTTTGGTGCTAAATGTATTGCT
GTTGGTGAGTCTGATGGGAGTATATGAAATCTAGATGGTTTTGACCCAAAGGAACTGGAAGACTTCAAATTGCAACATGG
GTCCATTCTGGGCTTCCCCAGGGCAAAGCCCTAGGAAGGAAGCATCTTGGAGGCTGACTGTGACATACTGACTCCCAGAT
GCCAGTGAGAAGCAGTTGACCAAATACAACACACCCAGAGTCAAAGCCAAGATTACTGATGAAGGTGCCAGCGGGCCAAC
AACTCCAGAAGCTGATAAGATCTTCCTGGAGGGAACATCACGGTTATTCCAGATCTCCACCTGAATTCTGGAGGAGTGAC
AGTATCATACTTTGAGTGGCTTAAGAATCTAAGTCATGTCAGCTATGGCCATTTGATCTTCAAATATGAAGGGGATTCTA
ACTACCACTTGCTCTTGTCTGTTCAAGAGAGT

Alignment

ORF - retro_cjac_2830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.32 %
• Parental protein coverage: 63.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSFPIRRDD-GSWEVIEGYRAQHSQHRTPCKGGIRYSTD-VSVDEVKALASLMTYKCAVVDVPFGGAKAG
          L..P.RR...G......G..AQHSQHRTP.KGGIR.ST...SVDEVKALASLMTYKCAVV.VPFGGA.AG
Retrocopy LPHPARRQLLGGHQRLGGHWAQHSQHRTPRKGGIRHSTA<LSVDEVKALASLMTYKCAVVNVPFGGANAG

Parental  VKINPKNY-TDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHAC
          V.INPKNY.TDNEL.KITRRFTMELAKKGFIGPGIDVPAPDM.TGE.EMSWI.D.YASTIGH..INAHAC
Retrocopy VEINPKNYYTDNELDKITRRFTMELAKKGFIGPGIDVPAPDMNTGEGEMSWIPDIYASTIGHCNINAHAC

Parental  VTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVG-LHSMRYLHRF
          VTGKPISQGGIHGRISATG.GVFHG.ENFI.EASYMSILGMTPGFGDKTFVVQGFG..G......YLHRF
Retrocopy VTGKPISQGGIHGRISATGHGVFHGVENFISEASYMSILGMTPGFGDKTFVVQGFG*CG<AYTL*YLHRF

Parental  GAKCIAVGESDGSIWNPDGIDPKELEDFKLQHGSILGFPKAKPYEGSILEADCDIL-IPAASEKQLTKSN
          GAKCIAVGESDGSI.N.DG.DPKELEDFKLQHGSILGFP.AKP.EGSILEADCDIL..P.ASEKQLTK.N
Retrocopy GAKCIAVGESDGSI*NLDGFDPKELEDFKLQHGSILGFPRAKP*EGSILEADCDIL>LPDASEKQLTKYN

Parental  APRVKAKIIAEGANGPTTPEADKIFLE-RNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERD
          .PRVKAKI..EGA.GPTTPEADKIFLE..NI.VIPDL.LN.GGVTVSYFEWLKNL.HVSYG.L.FKYE.D
Retrocopy TPRVKAKITDEGASGPTTPEADKIFLE<GNITVIPDLHLNSGGVTVSYFEWLKNLSHVSYGHLIFKYEGD

Parental  SNYHLLMSVQES
          SNYHLL.SVQES
Retrocopy SNYHLLLSVQES

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	0.00 RPM	42.27 RPM
SRP051959_heart	0.00 RPM	65.69 RPM
SRP051959_kidney	0.07 RPM	138.46 RPM
SRP051959_liver	0.06 RPM	398.97 RPM
SRP051959_lung	0.02 RPM	47.74 RPM
SRP051959_lymph_node	0.00 RPM	49.50 RPM
SRP051959_skeletal_muscle	0.00 RPM	28.45 RPM
SRP051959_spleen	0.00 RPM	54.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2830 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2830 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2830 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830 ,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,