RetrogeneDB ID: retro_cjac_2890

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:66192112..66192459(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006575
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012795
• Aliases: None
• Description: None

Sequence

>retro_cjac_2890
ATGGCCAGTACAATGGTAGCAGTTGGACTGACCATTGCAGCTGCAGGATTTGCAGGCCGTTATGTTTTGCAAGCATGAAG
CATATGGAACCTCAAGTAAAACAAGTTTTTCAAAGTCTACCAAAATCTGCCTTCAGTGGTGGCTATTACAGAGGCAGGTT
TGAACCCAAAATGACAAAACGGGAAGCAGCATTAATACTAGGTATAAGCCCTACTGCCAATAAAGGGAAAATAAGAGATG
CTCATCGACAAATTATGCTTTTAAATTATCCTGACAAAGGAGGATCCCCTTATATTGCAGCCAAAATCAATGAAGCTAAA
GATCTACTAGAAGGTCAAGCTAAAAAA

Alignment

ORF - retro_cjac_2890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASTMVAVGLTIAAAGFAGRYVLQA-MKHMEPQVKQVFQSLPKSAFSGGYYRGGFEPKMTKREAALILGV
          MASTMVAVGLTIAAAGFAGRYVLQA.MKHMEPQVKQVFQSLPKSAFSGGYYRG.FEPKMTKREAALILG.
Retrocopy MASTMVAVGLTIAAAGFAGRYVLQA<MKHMEPQVKQVFQSLPKSAFSGGYYRGRFEPKMTKREAALILGI

Parental  SPTANKGKIRDAHRRIMLLNHPDKGGSPYIAAKINEAKDLLEGQAKK
          SPTANKGKIRDAHR.IMLLN.PDKGGSPYIAAKINEAKDLLEGQAKK
Retrocopy SPTANKGKIRDAHRQIMLLNYPDKGGSPYIAAKINEAKDLLEGQAKK

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	12.94 RPM
SRP051959_heart	0.00 RPM	19.72 RPM
SRP051959_kidney	0.00 RPM	27.20 RPM
SRP051959_liver	0.00 RPM	42.74 RPM
SRP051959_lung	0.02 RPM	15.88 RPM
SRP051959_lymph_node	0.00 RPM	17.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	42.26 RPM
SRP051959_spleen	0.00 RPM	17.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2890 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2890 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 34 parental genes, and 172 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012255	6 retrocopies	retro_amel_1087, retro_amel_155, retro_amel_252, retro_amel_283, retro_amel_744, retro_amel_994,
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Canis familiaris	ENSCAFG00000032714	8 retrocopies	retro_cfam_1256, retro_cfam_1306, retro_cfam_1451, retro_cfam_2015, retro_cfam_346, retro_cfam_389, retro_cfam_741, retro_cfam_819,
Callithrix jacchus	ENSCJAG00000012795	10 retrocopies	retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890 , retro_cjac_3060, retro_cjac_914,
Callithrix jacchus	ENSCJAG00000017589	2 retrocopies	retro_cjac_1663, retro_cjac_634,
Cavia porcellus	ENSCPOG00000021198	1 retrocopy	retro_cpor_126,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Dipodomys ordii	ENSDORG00000005862	7 retrocopies	retro_dord_232, retro_dord_295, retro_dord_320, retro_dord_53, retro_dord_586, retro_dord_684, retro_dord_794,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi	ENSETEG00000006897	7 retrocopies	retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis	ENSFALG00000008296	1 retrocopy	retro_falb_28,
Felis catus	ENSFCAG00000010591	7 retrocopies	retro_fcat_1250, retro_fcat_1481, retro_fcat_1603, retro_fcat_1837, retro_fcat_475, retro_fcat_511, retro_fcat_982,
Homo sapiens	ENSG00000205981	8 retrocopies	retro_hsap_1330, retro_hsap_2061, retro_hsap_2062, retro_hsap_2349, retro_hsap_3497, retro_hsap_387, retro_hsap_538, retro_hsap_583,