RetrogeneDB ID: retro_cjac_3316

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:74736421..74737065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014458
• Aliases: None
• Description: None

Sequence

>retro_cjac_3316
CAGAGGCTAACTCAGGTGAGGTGGAGCTGCTATAGTGCTGAATTCAAGGATCCCCTGATTGACAGGGAACATTATCGCAA
GCCCGTGGAGAAGCTAACTGAGGAGAAATACGATAAGGAGCTCAAGAAGACTCAGCTCATCAAAGCTGCTCCAGCAGCAA
AAACAAGTTCTGTGTTTGAAGACCCAGTCGTCAGTAAATTCAGCAACATGACGGTGAAAGGAGGAAACAAAATACTGGCC
AGATCCCGCATGACTCAGACTCTGGAAGCTGTGAAAAGGAAGCAGTTTGAGAAGTACTATGCCCCTTCTGCAGAGGAACA
GGCAACCACTGAACAGAACCCATACACCATCTTCCGCCAAGCACTGAAAAACTGTGAGCCTATGATTGGGCTGGTAACCA
TCCTCAGAGGAGGCCGTTTCTACCAGGTCACTGTACCCCTACCCGACCGACGTTGCTGCTTCCTGGCCATGAAGTGGATG
ATCACTGAGTGCCGGGAGAACAAGCATAGGTGGACTCTGATGCCGGAGAAACGGTCCACGAGCTGCTGGAGGCTTTTCAT
AACCAGGGCCCTGTGATCAAGAGGAAGCATGGCATGCACAAGATGGCTGAGGCCAACCGTGCCGTGGCCCACTACCGCTG
GTGG

Alignment

ORF - retro_cjac_3316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.18 %
• Parental protein coverage: 89.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERLTQVRWSRYSAEFKDPLIDKEHYRKPVEKLTEEEKYDRELKKTQLIKAAPAAKTSSVFEDPVVSKFTN
          .RLTQVRWS.YSAEFKDPLID.EHYRKPVEKLTEE.KYD.ELKKTQLIKAAPAAKTSSVFEDPVVSKF.N
Retrocopy QRLTQVRWSCYSAEFKDPLIDREHYRKPVEKLTEE-KYDKELKKTQLIKAAPAAKTSSVFEDPVVSKFSN

Parental  MMMKGGNKILARSLMTQTLESVKRKQFEKYHAASAEEQATIERNPYIIFHQALRNCEPMIGLVPILRGGR
          M..KGGNKILARS.MTQTLE.VKRKQFEKY.A.SAEEQAT.E.NPY.IF.QAL.NCEPMIGLV.ILRGGR
Retrocopy MTVKGGNKILARSRMTQTLEAVKRKQFEKYYAPSAEEQATTEQNPYTIFRQALKNCEPMIGLVTILRGGR

Parental  IYQVPTSLPDRRRRFLAMKWMITECRENKHRRMLMPEKLS-HELLEAFHNQGPVIKRKHDMHKMAEANRA
          .YQV...LPDRR..FLAMKWMITECRENKHR..LMPEK.S.HELLEAFHNQGPVIKRKH.MHKMAEANRA
Retrocopy FYQVTVPLPDRRCCFLAMKWMITECRENKHRWTLMPEKRS<HELLEAFHNQGPVIKRKHGMHKMAEANRA

Parental  LAHYRWW
          .AHYRWW
Retrocopy VAHYRWW

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	0.00 RPM	6.39 RPM
SRP051959_heart	0.00 RPM	10.84 RPM
SRP051959_kidney	0.00 RPM	11.38 RPM
SRP051959_liver	0.00 RPM	10.01 RPM
SRP051959_lung	0.00 RPM	7.22 RPM
SRP051959_lymph_node	0.00 RPM	6.28 RPM
SRP051959_skeletal_muscle	0.02 RPM	24.04 RPM
SRP051959_spleen	0.00 RPM	7.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3316 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3316 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316 ,
Erinaceus europaeus	ENSEEUG00000015775	1 retrocopy	retro_eeur_212,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013, retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Oryctolagus cuniculus	ENSOCUG00000017928	1 retrocopy	retro_ocun_609,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,
Ictidomys tridecemlineatus	ENSSTOG00000015200	2 retrocopies	retro_itri_1805, retro_itri_461,