RetrogeneDB ID: retro_cjac_1705

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:26274085..26274332(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000016978
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSCJAG00000002705
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_cjac_1705
ATGAGTTTACCCCTCAGTCTTAAATCTTTCCTCAGTGGATTAACAGGAAAGCCAGTGATGGTGAAGCTTAAGTGGGGGAA
TGAGTACAAGGGCTACTTGGTGTCTGTACATGGCTACATGAACATGCAGCGTGCAGATACAGAACTCATAAATGAGGCAT
TATCTGGACATCTAGGTGAAGTTTTAGTAAGGTGGAAATAATGTCCTTTATATCAGAGGTGTGGAAGAAGAGGAATGGGG
AAATGAA

Alignment

ORF - retro_cjac_1705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 96.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRC-NNV
          MSLPL..K.FL.GLTGKPVMVKLKWG.EYKGYLVSV.GYMNMQ.A.T.E.I..ALSGHLGEVL.R..NNV
Retrocopy MSLPLSLKSFLSGLTGKPVMVKLKWGNEYKGYLVSVHGYMNMQRADT-ELINEALSGHLGEVLVRW>NNV

Parental  LYIRGVEEEEEDGE
          LYIRGVEEEE...E
Retrocopy LYIRGVEEEEWGNE

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	5.79 RPM
SRP051959_heart	0.00 RPM	5.63 RPM
SRP051959_kidney	0.02 RPM	6.37 RPM
SRP051959_liver	0.00 RPM	4.27 RPM
SRP051959_lung	0.02 RPM	5.86 RPM
SRP051959_lymph_node	0.00 RPM	6.55 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.53 RPM
SRP051959_spleen	0.00 RPM	6.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1705 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1705 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1705 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_550

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Canis familiaris	ENSCAFG00000006395	6 retrocopies	retro_cfam_110, retro_cfam_1975, retro_cfam_372, retro_cfam_619, retro_cfam_742, retro_cfam_763,
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176, retro_cjac_3248,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705 , retro_cjac_3039,
Erinaceus europaeus	ENSEEUG00000013509	4 retrocopies	retro_eeur_241, retro_eeur_465, retro_eeur_467, retro_eeur_636,
Echinops telfairi	ENSETEG00000001558	3 retrocopies	retro_etel_1765, retro_etel_1846, retro_etel_560,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Latimeria chalumnae	ENSLACG00000002456	1 retrocopy	retro_lcha_73,
Loxodonta africana	ENSLAFG00000017426	1 retrocopy	retro_lafr_241,
Monodelphis domestica	ENSMODG00000008091	3 retrocopies	retro_mdom_550, retro_mdom_780, retro_mdom_811,
Pelodiscus sinensis	ENSPSIG00000016462	2 retrocopies	retro_psin_31, retro_psin_54,
Sarcophilus harrisii	ENSSHAG00000012294	1 retrocopy	retro_shar_468,
Tarsius syrichta	ENSTSYG00000006837	4 retrocopies	retro_tsyr_1239, retro_tsyr_1782, retro_tsyr_192, retro_tsyr_2115,