RetrogeneDB ID: retro_cjac_2329

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:38177877..38178215(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000005468
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C19orf70
• Ensembl ID: ENSCJAG00000017076
• Aliases: None
• Description: chromosome 19 open reading frame 70 [Source:HGNC Symbol;Acc:33702]

Sequence

>retro_cjac_2329
ATGGTGGCCCGGGTGTGGCCGCTGATGAGGCTCCTCATCAAGGGGAGTGTGGCTGGAGGCACCATCTACCAGGAGCTGCT
GGGGCCCAGTGACAAGAGCCAGGCAGCCCTACAAAAGGCTGGGGAGGTGGTCCCTCCCGCCATGTACCAGTTCAGCCGGT
ACCTCGTCAGCAGACAGGCCAGCAGATAACCCAGCTCCCAGCCCCTCCAAAGATTCACTTTACCATCCGTGACTCCTGGA
ATGCAGGCATCATCACGGTGATGTCAGCTCTGTCAGTGGCCCCTTCCATGGCCCACGAGTACTCCAAGGAGGGCTGGGAG
TAGGTGAAGGCACGCACC

Alignment

ORF - retro_cjac_2329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.05 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVARVWSLMRFLIKGSVAGGAVYLVYDQELLGSSDKSQAALKKAGEVVPPAMYQFSHYVC-QQTGLQIPQ
          MVARVW.LMR.LIKGSVAGG..Y....QELLG.SDKSQAAL.KAGEVVPPAMYQFS.Y...QQTG.QI.Q
Retrocopy MVARVWPLMRLLIKGSVAGGTIY----QELLGPSDKSQAALQKAGEVVPPAMYQFSRYLV<QQTGQQITQ

Parental  LPAPPKIHFPIRDSWNAGIITVMSALSVAPSKACEYSKEGWEYVKART
          LPAPPKIHF.IRDSWNAGIITVMSALSVAPS.A.EYSKEGWE.VKART
Retrocopy LPAPPKIHFTIRDSWNAGIITVMSALSVAPSMAHEYSKEGWE*VKART

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	0.13 RPM	8.08 RPM
SRP051959_heart	0.07 RPM	9.30 RPM
SRP051959_kidney	0.09 RPM	8.50 RPM
SRP051959_liver	0.39 RPM	9.51 RPM
SRP051959_lung	0.42 RPM	6.33 RPM
SRP051959_lymph_node	0.64 RPM	7.10 RPM
SRP051959_skeletal_muscle	0.02 RPM	14.41 RPM
SRP051959_spleen	0.95 RPM	7.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2329 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2329 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018796	2 retrocopies	retro_cfam_1706, retro_cfam_756,
Callithrix jacchus	ENSCJAG00000017076	2 retrocopies	retro_cjac_2329 , retro_cjac_735,
Felis catus	ENSFCAG00000011836	1 retrocopy	retro_fcat_287,
Loxodonta africana	ENSLAFG00000026050	1 retrocopy	retro_lafr_1241,
Macaca mulatta	ENSMMUG00000028920	1 retrocopy	retro_mmul_251,
Monodelphis domestica	ENSMODG00000001268	1 retrocopy	retro_mdom_1960,
Mustela putorius furo	ENSMPUG00000006136	2 retrocopies	retro_mputfur_1001, retro_mputfur_217,
Procavia capensis	ENSPCAG00000006583	1 retrocopy	retro_pcap_106,
Tupaia belangeri	ENSTBEG00000013386	1 retrocopy	retro_tbel_1443,