RetrogeneDB ID: retro_cjac_4

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:104352157..104352835(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022647
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003168
• Aliases: None
• Description: None

Sequence

>retro_cjac_4
ATGTCGTGCCAGTCGTCTATGGTTCTGGGGTACTGGGATATTCGCGGGCTGGCGCACGCCATCCGCCTGCTCCTGGAGTT
CACCGATACCTCCTACAAGGAGAAACGTTACACGTGCGGGGAAGCTCCTGACTATGATCGAAGCCAATGGCTGGATGTGA
AATTCAAGCTAAACTTGGACTTTCCTAATCTGCCCTACCTCCTGGATGGGAAGAACAAAATCACCCAGAGCAATGCCATC
TTGCGCTACATCGCCCGCAAGCACAACATGTGTGGTGAGACTGAAGAGGAAAAGATACAAGTGGACATCGTAGAGAACCA
AGTAATGGATTTCCGCATACAACTGATAAAGCTCTGTTACAGCCCTGACCATGAAAAACTGAAGCCTCAGTACTTGGAAC
AGCTACCTGGACAACTGAAACAATTCTCCATGTTTTTGGGGAAATTCTCATGGTTTGCAGGGGAAAAGCTCACCTATGTG
GACTTTCTCACCTATGATATCTTGGATCAGAACCGTATATTTGAGCCCAAGTGCCTGGATGAGTTCCCAAACCTGAAGGC
TTTCATGGGCCGTTTTGAGGCTTTGGAGAAAATCGCTGCCTACATACAGTCTGATAACTTCTTCAAGATGCCCATCAACA
ACAAGATGGCCCAATGGGGCAACAAGGCTATATGCTGA

Alignment

ORF - retro_cjac_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSCQSSMVLGYWDIRGLAHAIRLLLEFTDTSYEEKRYTCGEAPDYDRSQWLDVKFKLNLDFPNLPYLLDG
          MSCQSSMVLGYWDIRGLAHAIRLLLEFTDTSY.EKRYTCGEAPDYDRSQWLDVKFKLNLDFPNLPYLLDG
Retrocopy MSCQSSMVLGYWDIRGLAHAIRLLLEFTDTSYKEKRYTCGEAPDYDRSQWLDVKFKLNLDFPNLPYLLDG

Parental  KNKITQSNAILRYIARKHNMCGETEEEKIRVDIVENQVMDFRIQLIKLCYSSDHEKLKPQYLEQLPGQLK
          KNKITQSNAILRYIARKHNMCGETEEEKI.VDIVENQVMDFRIQLIKLCYS.DHEKLKPQYLEQLPGQLK
Retrocopy KNKITQSNAILRYIARKHNMCGETEEEKIQVDIVENQVMDFRIQLIKLCYSPDHEKLKPQYLEQLPGQLK

Parental  QFSMFLGKFSWFAGEKLTYVDFLTYDILDQNRIFEPKCLDEFPNLKAFMGRFEALEKIAAYIQSDNFFKM
          QFSMFLGKFSWFAGEKLTYVDFLTYDILDQNRIFEPKCLDEFPNLKAFMGRFEALEKIAAYIQSDNFFKM
Retrocopy QFSMFLGKFSWFAGEKLTYVDFLTYDILDQNRIFEPKCLDEFPNLKAFMGRFEALEKIAAYIQSDNFFKM

Parental  PINNKMAQWGNKAIC
          PINNKMAQWGNKAIC
Retrocopy PINNKMAQWGNKAIC

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	1.42 RPM
SRP051959_heart	0.00 RPM	1.98 RPM
SRP051959_kidney	0.00 RPM	3.28 RPM
SRP051959_liver	0.04 RPM	7.21 RPM
SRP051959_lung	0.03 RPM	2.18 RPM
SRP051959_lymph_node	0.00 RPM	0.80 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.89 RPM
SRP051959_spleen	0.00 RPM	1.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004, retro_cjac_3084, retro_cjac_811,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4 ,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393, retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,