RetrogeneDB ID: retro_cjac_372

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:4583287..4584217(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023411
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020614
• Aliases: None
• Description: None

Sequence

>retro_cjac_372
ATGGCGGCGGCCGGGGCCCCGGATGGCATGGAGGAACCTGGCATGGACACGGAGGCCGAGACCGTGGCGACCGAGGCGCC
CGCGCGGTCCCTCAACTGCGTGGAGGCCGAAGCCGCGGCGGGGATGGCGGCCGAGGACTCTGGCGCCGCGCGAGACAACC
TGCAGCCGGCCCCGGCCCAGCCCCCTGGGGACCCTGTGGCCCAGGCCTCGGTCAGCAACGGCGAAGACGCAGGCGGCGGC
GCGGGCAAGGAGCTGGTGGACCTGAAGATCATCTGGAACGAGACCAAGCACGACGTGAAGGTCCCCTTGGACAGCACAGG
CTCCGAACTGAAACAGAAGATCCACTCGATTACAGGTCTCCCGCCTGCCATGCAGAAAGTCATGTATAAGGGACTCGTCC
CCGAGGATAAGACATTGAGAGAAATCAAAGTGACCAGCGGGGCCAAGATCATGGTGGTTGGCTCCACCATCAATGATGTT
TTAGCAGTAAACACACCCAAAGATGCTGTGCAGCAGGATGCAAAGGCCGAAGAGAACAAGAAGGAGCCTCTCTGCAGGCA
GAAACAACACAGGAAAGTGTTGGATAAAGGAAAACCTGAAGATGTGATGCCATCTGTTAAGGGTGCCCAGGAGCGCCTGC
CAACGGTACCCCTGTCCGGCATGTACAATAAGTCCGGAGGAAAAGTGAGACTCGCCTTTAAGCTAGAACAAGACCAACTG
TGGATTGGCACTAAAGAGCGGACTGAGAAATTGCCCATGGGCTCCATAAAAAATGTGGTCAGTGAACCTATGGAAGGACA
TGAAGACTACCACATGATGGCGTTTCAGTTGGGCCCCACGGAAGCCTCTTACTACTGGGTGTACTGGGTTCCAACTCAAT
ATGTGGATGCAATCAAAGACACTGTGCTGGGGAAATGGCAGTATTTTTGA

Alignment

ORF - retro_cjac_372 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APAQPPGDPVAQASVSN-EDAGGGAGKELVDLKIIWNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQK
          APAQPPGDPVAQASVSN.EDAGGGAGKELVDLKIIWN.TKHDVKVPLDSTGSELKQKIHSITGLPPAMQK
Retrocopy APAQPPGDPVAQASVSNGEDAGGGAGKELVDLKIIWNETKHDVKVPLDSTGSELKQKIHSITGLPPAMQK

Parental  VMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKDAVQQDAKAEENKKEPLCRQKQHRKVLDK
          VMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKDAVQQDAKAEENKKEPLCRQKQHRKVLDK
Retrocopy VMYKGLVPEDKTLREIKVTSGAKIMVVGSTINDVLAVNTPKDAVQQDAKAEENKKEPLCRQKQHRKVLDK

Parental  GKPEDVMPSVKGAQERLPTVPLSGMYNKSGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIEG
          GKPEDVMPSVKGAQERLPTVPLSGMYNKSGGKVRL.FKLEQDQLWIGTKERTEKLPMGSIKNVVSEP.EG
Retrocopy GKPEDVMPSVKGAQERLPTVPLSGMYNKSGGKVRLAFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPMEG

Parental  HEDYHMMVSSTG
          HEDYHMM....G
Retrocopy HEDYHMMAFQLG

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	0.47 RPM	3.84 RPM
SRP051959_heart	0.44 RPM	4.31 RPM
SRP051959_kidney	0.51 RPM	4.24 RPM
SRP051959_liver	0.56 RPM	4.03 RPM
SRP051959_lung	0.78 RPM	3.30 RPM
SRP051959_lymph_node	0.53 RPM	3.52 RPM
SRP051959_skeletal_muscle	0.68 RPM	4.00 RPM
SRP051959_spleen	0.36 RPM	4.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_372 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_372 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029331	2 retrocopies	retro_acar_106, retro_acar_204,
Canis familiaris	ENSCAFG00000017670	1 retrocopy	retro_cfam_1952,
Callithrix jacchus	ENSCJAG00000020614	1 retrocopy	retro_cjac_372 ,
Cavia porcellus	ENSCPOG00000006872	2 retrocopies	retro_cpor_292, retro_cpor_635,
Monodelphis domestica	ENSMODG00000006727	2 retrocopies	retro_mdom_1162, retro_mdom_1298,
Oryctolagus cuniculus	ENSOCUG00000008444	1 retrocopy	retro_ocun_666,