RetrogeneDB ID: retro_cjac_1003

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:98655477..98655772(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018888
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004427
• Aliases: None
• Description: None

Sequence

>retro_cjac_1003
ATGGCACAGGGGCAATGTAAGTTGCAGGCGCACAAGCCATCGAAGAGGCAGCGGGGGCGGCCTCTGAAAGGGACCAGGGC
CCTAGGAAAGGAGGTCGTGTTATGCTCCCAAGAAGGCACGCGTCGTTCAGCAGCAAAAGCTCAAGAAGAACCGAGAAGTT
GGGATCTGGAAGAAGATTGAACATGACGTGGTGAGGAAAGTCAGCAACAGCCTGCCCAAGAAGCTGGCACCGCTGAAGGC
CCTGGCCAAGAAGAAGGGGGCGGCTGCCGCCACCTCTTCCAACAAGACGCTTTCC

Alignment

ORF - retro_cjac_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAQGQRKFQAHKPAKSK-TAAAASEKNRGPRKGGRVI-APKKARVVQQQKLKKNLEVGIRKKIEHDVMMK
          MAQGQ.K.QAHKP.K.....AA.SE...GPRKGGRV..APKKARVVQQQKLKKN.EVGI.KKIEHDV..K
Retrocopy MAQGQCKLQAHKPSKRQ<AGAA-SERDQGPRKGGRVM<APKKARVVQQQKLKKNREVGIWKKIEHDVVRK

Parental  AS-CLPKKLALLKAPAKNR-AAATTSSNKAPS
          .S..LPKKLA.LKA.AK...AAA.TSSNK..S
Retrocopy VSNSLPKKLAPLKALAKKKGAAAATSSNKTLS

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	5.59 RPM
SRP051959_heart	0.00 RPM	5.49 RPM
SRP051959_kidney	0.02 RPM	7.28 RPM
SRP051959_liver	0.02 RPM	8.06 RPM
SRP051959_lung	0.02 RPM	6.72 RPM
SRP051959_lymph_node	0.00 RPM	7.05 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.32 RPM
SRP051959_spleen	0.06 RPM	6.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1003 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1003 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002525	1 retrocopy	retro_btau_35,
Callithrix jacchus	ENSCJAG00000004427	3 retrocopies	retro_cjac_1003 , retro_cjac_2634, retro_cjac_291,
Homo sapiens	ENSG00000104979	1 retrocopy	retro_hsap_628,
Gorilla gorilla	ENSGGOG00000027024	1 retrocopy	retro_ggor_550,
Monodelphis domestica	ENSMODG00000011876	2 retrocopies	retro_mdom_1436, retro_mdom_926,
Nomascus leucogenys	ENSNLEG00000013141	1 retrocopy	retro_nleu_452,
Otolemur garnettii	ENSOGAG00000007185	1 retrocopy	retro_ogar_640,
Procavia capensis	ENSPCAG00000014250	1 retrocopy	retro_pcap_26,
Pan troglodytes	ENSPTRG00000010565	1 retrocopy	retro_ptro_457,
Pteropus vampyrus	ENSPVAG00000006321	1 retrocopy	retro_pvam_1140,
Tursiops truncatus	ENSTTRG00000010354	1 retrocopy	retro_ttru_317,