RetrogeneDB ID: retro_cjac_219

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:96092671..96093436(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022998
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014547
• Aliases: None
• Description: None

Sequence

>retro_cjac_219
ATGAGTCGTCGCTGGGCTTGGCGGTTCTTGCTTTTCCAAGGCAGCGGAGATCGCTGGGTTTCAAGCCCCCGCGGGCATTT
CTCGCCGGCCCTGCGGAGAGACTTCTTCACTATCACAACCAAAGAGGGATATGATAGGCGTCCAGTGGACATAACTCCTT
TAGAACAAAGGAAATTAACTTTTGATACCCATGCATTGGTTCAGGACTTGGAAACTCATGGATTTGACAAAACACAAGCA
GAAACAATTGTATCAGCATTAACTACTTTATCAAATGTCAGCCTGGATACTATCTATAAAGAGATGATCACTCAAGCTCA
ACAGGAAATAACAGTACAACAGCTAATGGCTCATTTGGACTCTATCAGGAAAGACATGGTCATCCTAGAGAAAAGTGAAT
TTGCAAATCTGAGAGCTGAGAATGAGAAAATGAAAATTGAACTAGACCAAGTTAAGCAACAACTAATGCATGAAACCAGT
CGAATCAGAGCAGATAATAAACTGGGTATCAACCTAGAAAGGAGCAGAGTAACAGATATGTTTACAGATCAAGAAAAGCA
ACTTATGGAAGCAACTACAGAATTTACAAAAAAAGATACCCAAACCAAAAGTATTATTTCAGAGACCAGTAATAAAATTG
ATGCTGAAATTGCTTCCTTAAAAACACTGATGGAGTCTAACAAACTTGAGACCATTCGTTATCTTGCAGCCTCAGTGTTT
ACTTGCCTGGCAATAGCATTGGGATTTTATAGATTCTGGAAGTAG

Alignment

ORF - retro_cjac_219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRRRAWRFLLFQGSGDRWVSSPRGHFSPALRRGFFTTTTKEGYDRRPVDITPLEQRKLTFDTHALVQDL
          MSRR.AWRFLLFQGSGDRWVSSPRGHFSPALRR.FFT.TTKEGYDRRPVDITPLEQRKLTFDTHALVQDL
Retrocopy MSRRWAWRFLLFQGSGDRWVSSPRGHFSPALRRDFFTITTKEGYDRRPVDITPLEQRKLTFDTHALVQDL

Parental  ETHGFDKTQAETIVSALTTLSNVSLDTIYKEMVTQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAE
          ETHGFDKTQAETIVSALTTLSNVSLDTIYKEM.TQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAE
Retrocopy ETHGFDKTQAETIVSALTTLSNVSLDTIYKEMITQAQQEITVQQLMAHLDSIRKDMVILEKSEFANLRAE

Parental  NEKMKIELDQVKQQLMHETSRIRADNKLDINLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETS
          NEKMKIELDQVKQQLMHETSRIRADNKL.INLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETS
Retrocopy NEKMKIELDQVKQQLMHETSRIRADNKLGINLERSRVTDMFTDQEKQLMEATTEFTKKDTQTKSIISETS

Parental  NKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRFWK
          NKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRFWK
Retrocopy NKIDAEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRFWK

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	0.16 RPM	4.13 RPM
SRP051959_heart	0.25 RPM	6.52 RPM
SRP051959_kidney	0.47 RPM	6.74 RPM
SRP051959_liver	0.26 RPM	5.52 RPM
SRP051959_lung	0.33 RPM	6.28 RPM
SRP051959_lymph_node	0.27 RPM	5.00 RPM
SRP051959_skeletal_muscle	0.35 RPM	5.39 RPM
SRP051959_spleen	0.29 RPM	6.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_219 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_219 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219 ,
Callithrix jacchus	ENSCJAG00000016050	1 retrocopy	retro_cjac_2522,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880, retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366,