RetrogeneDB ID: retro_cjac_1834

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:122223044..122223760(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011132
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRTO4
• Ensembl ID: ENSCJAG00000006812
• Aliases: None
• Description: mRNA turnover 4 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:18477]

Sequence

>retro_cjac_1834
ATGCCCAAATCCAAACGCGACAAGAAAGTCTCCTTAACCAAAACTGCCAAGAAGGGCTTGGAATTGAAACAAAACCTGAT
AGAAGAGCTTCGGAAATGTGTGGACACTTACAAGTACCTTTTCATCTTCTCTGTGGCCAACATGAGAAATAGCAAGCTGA
AGGACATCTGGAACGCCTGGAAGCACAGCCGGATGTTCTTTGGCAAAAACAAGGTAATGATGGTGGCCTTGGGTCGGAGC
CCATCTGATGAGTACAAAGACAACCTGCACCAGGTCAGCAAAAAGTTGAGGGTGAAGTGGGTCTCCTGTTCACCAACCGC
ACAAAGGAGGAGGTGAATGAATGGTTCACGAAATACACAGAAATGGACTATGCCCGAGCTGGTAACAAAGCAACTTTCAC
TGTGAGCTTGGACTCAGGGCCCCTGGAGCAGTTCCCCCACTCCATGGAGCCACAGCTGAGGCAGCTGGGCCTGCCCACCA
CCCTCAAAAGAGGTGTGGTGACCCTGCTGTCCGACTACGAGGTGTGCAAGGAGGGTGACGTGCTGACCCCAGAGCAGGCT
CGCGTCCTGAAGCTTTTTGGGTATGAGATGGCTGAATTCAAGGTGACCATCAAATACATGTGGGACTCACAGTCGGGAAG
TTTCCAGCAGATGGGAGATGACTTGCCAGAGAGCGCATCCGAGTCTGCAGAAGACTCAGAGTTAGAAGACAGTGAC

Alignment

ORF - retro_cjac_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIRNAWKHSRMFFGKN
          MPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDI.NAWKHSRMFFGKN
Retrocopy MPKSKRDKKVSLTKTAKKGLELKQNLIEELRKCVDTYKYLFIFSVANMRNSKLKDIWNAWKHSRMFFGKN

Parental  KVMMVALGRSPSDEYKDNLHQVSKKLR-GEVGLLFTNRTKEEVNEWFTKYTEMDYARAGNKATFTVSLDS
          KVMMVALGRSPSDEYKDNLHQVSKKLR.GEVGLLFTNRTKEEVNEWFTKYTEMDYARAGNKATFTVSLDS
Retrocopy KVMMVALGRSPSDEYKDNLHQVSKKLR<GEVGLLFTNRTKEEVNEWFTKYTEMDYARAGNKATFTVSLDS

Parental  GPLEQFPHSMEPQLRQLGLPTTLKRGVVTLLSDYEVCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWD
          GPLEQFPHSMEPQLRQLGLPTTLKRGVVTLLSDYEVCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWD
Retrocopy GPLEQFPHSMEPQLRQLGLPTTLKRGVVTLLSDYEVCKEGDVLTPEQARVLKLFGYEMAEFKVTIKYMWD

Parental  SQSGRFQQMGDDLPESASESAEDSELEDSD
          SQSG.FQQMGDDLPESASESAEDSELEDSD
Retrocopy SQSGSFQQMGDDLPESASESAEDSELEDSD

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	0.07 RPM	6.21 RPM
SRP051959_heart	0.21 RPM	6.88 RPM
SRP051959_kidney	0.33 RPM	9.50 RPM
SRP051959_liver	0.17 RPM	14.47 RPM
SRP051959_lung	0.15 RPM	6.02 RPM
SRP051959_lymph_node	0.16 RPM	7.33 RPM
SRP051959_skeletal_muscle	0.28 RPM	14.28 RPM
SRP051959_spleen	0.13 RPM	6.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1834 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015189	1 retrocopy	retro_cfam_1353,
Callithrix jacchus	ENSCJAG00000006812	3 retrocopies	retro_cjac_1146, retro_cjac_1834 , retro_cjac_3791,
Dasypus novemcinctus	ENSDNOG00000010119	6 retrocopies	retro_dnov_1051, retro_dnov_1545, retro_dnov_170, retro_dnov_1890, retro_dnov_2044, retro_dnov_2255,
Echinops telfairi	ENSETEG00000001675	5 retrocopies	retro_etel_1080, retro_etel_1162, retro_etel_1172, retro_etel_1887, retro_etel_2177,
Homo sapiens	ENSG00000053372	2 retrocopies	retro_hsap_1766, retro_hsap_1914,
Gorilla gorilla	ENSGGOG00000000533	2 retrocopies	retro_ggor_1400, retro_ggor_2244,
Macropus eugenii	ENSMEUG00000000027	1 retrocopy	retro_meug_1606,
Microcebus murinus	ENSMICG00000004019	2 retrocopies	retro_mmur_1235, retro_mmur_733,
Myotis lucifugus	ENSMLUG00000001566	1 retrocopy	retro_mluc_374,
Macaca mulatta	ENSMMUG00000006695	1 retrocopy	retro_mmul_107,
Monodelphis domestica	ENSMODG00000015874	1 retrocopy	retro_mdom_1694,
Mustela putorius furo	ENSMPUG00000016181	2 retrocopies	retro_mputfur_1177, retro_mputfur_1430,
Mus musculus	ENSMUSG00000028741	2 retrocopies	retro_mmus_852, retro_mmus_924,
Oryctolagus cuniculus	ENSOCUG00000000274	2 retrocopies	retro_ocun_1191, retro_ocun_951,
Otolemur garnettii	ENSOGAG00000010713	2 retrocopies	retro_ogar_1826, retro_ogar_2060,
Pongo abelii	ENSPPYG00000001795	2 retrocopies	retro_pabe_1535, retro_pabe_1548,
Pan troglodytes	ENSPTRG00000000262	2 retrocopies	retro_ptro_1182, retro_ptro_1248,
Rattus norvegicus	ENSRNOG00000017979	1 retrocopy	retro_rnor_2967,
Ictidomys tridecemlineatus	ENSSTOG00000028112	1 retrocopy	retro_itri_1551,
Tupaia belangeri	ENSTBEG00000006502	8 retrocopies	retro_tbel_1020, retro_tbel_1189, retro_tbel_1210, retro_tbel_1873, retro_tbel_1945, retro_tbel_2665, retro_tbel_394, retro_tbel_559,