RetrogeneDB ID: retro_cjac_309

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:40054495..40055335(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022714
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001981
• Aliases: None
• Description: None

Sequence

>retro_cjac_309
ATGACGAAGAACGAGAAAAAGTCCCTCAACCAGTGCCTGGCCGAGTGGAAGCTCTTCATTTACAACCCGACCACCGGAGA
GTTCCTGGGGCGCACCGCCAAGAGCTGGGGTTTGATCTTGCTCTTCTACCTAGTTTTTTATGGGTTCCTGGCTGCACTCT
TCTCATTCACGATGTGGGTTATGCTTCAGACTCTCAACGATGAGGTTCCAAAATATCGTGACCAGATTCCTAGCCCAGGA
CTTATGGTTTTTCCAAAACCAGTGACTGCATTGGAATACACATTCAGTGTGTCTGACCCAACTTCCTATGCAGGGTACAT
TGCAGACCTGAAGAAGTTTCTAAAACCATATACTTTAGAAGAACAGAAGAACCTCACAACCTGTCCTGATGGAGCACTTT
TTGAACAGAAGGGTCCCGTTTATGTTGCATGTCAGTTTCCTCTTTTGTTACTTCAAGCATGCAGCGGTATGAGTGATCCT
AATTTTGGCTATTCTAAAGGAAAACCTTGTATTCTTGTGAAAATGAACAGAATAATTGGATTAAAGCCTGAAGGAGTGCC
AAGGATAGATTGTGTTTTGAAGAATGAAGATCAAACAAATATAACAACTTATCCTCATAATGGAATGATAGACTTAAAAT
ATTTCCCATATTATGGGAAAAAACTGCATGTAGGGTATCTACAGCCATTAGTTGCTGTTCAGGTCACCTTGGCTCCCAAC
AGTGCTGAGAAAGAAGTAACAGTTGAGTGCAAGATTGATGGATCGCCTAACCTAAAAAGCCTGGATGATCGTGACAAGTT
TTTGGGACGAGTTATGTTCAAAATCACAGCACATGCATAG

Alignment

ORF - retro_cjac_309 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LILLFYLVFYGFLAALFSFTMWVMLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSVSDPTSYAGYI
          LILLFYLVFYGFLAALFSFTMWVMLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSVSDPTSYAGYI
Retrocopy LILLFYLVFYGFLAALFSFTMWVMLQTLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSVSDPTSYAGYI

Parental  ADLKKFLKPYTLEEQKNLTTCPDGALFEQKGPVYVACQFPLLLLQACSGMSDPDFGYSKGKPCILVKMNR
          ADLKKFLKPYTLEEQKNLTTCPDGALFEQKGPVYVACQFPLLLLQACSGMSDP.FGYSKGKPCILVKMNR
Retrocopy ADLKKFLKPYTLEEQKNLTTCPDGALFEQKGPVYVACQFPLLLLQACSGMSDPNFGYSKGKPCILVKMNR

Parental  IIGLKPEGVPRIDCVLKNEDQTNITTYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVTLAPSSAEKEVT
          IIGLKPEGVPRIDCVLKNEDQTNITTYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVTLAP.SAEKEVT
Retrocopy IIGLKPEGVPRIDCVLKNEDQTNITTYPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVTLAPNSAEKEVT

Parental  VECKIDGSPNLKSQDDRDKFLGRVMFKITAHA
          VECKIDGSPNLKS.DDRDKFLGRVMFKITAHA
Retrocopy VECKIDGSPNLKSLDDRDKFLGRVMFKITAHA

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	3.71 RPM	35.10 RPM
SRP051959_heart	0.70 RPM	4.63 RPM
SRP051959_kidney	0.69 RPM	5.57 RPM
SRP051959_liver	0.28 RPM	2.75 RPM
SRP051959_lung	1.43 RPM	11.75 RPM
SRP051959_lymph_node	1.42 RPM	14.41 RPM
SRP051959_skeletal_muscle	0.15 RPM	2.10 RPM
SRP051959_spleen	1.13 RPM	10.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_309 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309 ,
Callithrix jacchus	ENSCJAG00000010317	1 retrocopy	retro_cjac_2288,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571, retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,