RetrogeneDB ID: retro_cjac_2779

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:149236945..149237503(+)
• Located in intron of: ENSCJAG00000013816

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: POGK
• Ensembl ID: ENSCJAG00000033914
• Aliases: None
• Description: None

Sequence

>retro_cjac_2779
ATAGAGTCCGCAGTCTACCCTCTCAATTTGACCCTGAAAGAAGAGGAAGAGGAAGAAGAGATTCAGAGCCGGGAACTGGA
AGACTGCCCAGTTGTCATGCAGAAAGTCCGAATCTGCTCTGAGGGAGGATGGGTACCAGCCCTGTTTGATGAGGTGACCA
TATATTTTTCCAATGAGCAGTGGGAAGTTTTGACGGAGCAACAAAAGGCCCTGTACCAGGAAGTCATGAGGATGAATTAT
GAAACCGTCCTATCCCTGGAATTCCCATTCCCTAAGCCAGACATGATCACCCGGTTGGAAGGGGAGGAGGAGTCTCAGAA
TTCTGACGAGTGGCAACTCCAAGGAGGCATCTCTGCAGAAAATGAAGAATCTGATGTCAAGCCTCTAGACTGGCCAAGCC
CAATGAGTGCTACCTCCCACTTTCCTCAGCTTCAGCACTTCGACAGCTTTGGCCTCCGTCTGCCTTGGGATATCACAGAG
CTGCCTGAGTAGTGTGAGGGGTTCCCCTCCTACATGGCCATGGGCTTCCCAGGGTATGACCTCTCAACTGATGACATA

Alignment

ORF - retro_cjac_2779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.32 %
• Parental protein coverage: 89.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESAAYPLNLTLKEEEEEEEIQSRELEDGPVVMQKVRICSEGGWVPALFDEVAIYFSDEEWEVLTEQQKA
          .ESA.YPLNLTLKEEEEEEEIQSRELED.PVVMQKVRICSEGGWVPALFDEV.IYFS.E.WEVLTEQQKA
Retrocopy IESAVYPLNLTLKEEEEEEEIQSRELEDCPVVMQKVRICSEGGWVPALFDEVTIYFSNEQWEVLTEQQKA

Parental  LYREVMRMNYETVLSLEFPFPKPDMITRLEGEEESQNSDEWQLQGGTSAENEESDVKPPDWPSPVNATSH
          LY.EVMRMNYETVLSLEFPFPKPDMITRLEGEEESQNSDEWQLQGG.SAENEESDVKP.DWPSP..ATSH
Retrocopy LYQEVMRMNYETVLSLEFPFPKPDMITRLEGEEESQNSDEWQLQGGISAENEESDVKPLDWPSPMSATSH

Parental  FPQPQHFDSFGLRLPRDITELPEWSEGYPFYMAMGFPGYDLSADDI
          FPQ.QHFDSFGLRLP.DITELPE..EG.P.YMAMGFPGYDLS.DDI
Retrocopy FPQLQHFDSFGLRLPWDITELPE*CEGFPSYMAMGFPGYDLSTDDI

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	1.20 RPM	3.04 RPM
SRP051959_heart	0.67 RPM	4.21 RPM
SRP051959_kidney	1.20 RPM	5.21 RPM
SRP051959_liver	0.78 RPM	2.69 RPM
SRP051959_lung	1.01 RPM	4.72 RPM
SRP051959_lymph_node	1.39 RPM	5.14 RPM
SRP051959_skeletal_muscle	1.18 RPM	1.59 RPM
SRP051959_spleen	1.18 RPM	4.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2779 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2779 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033914	1 retrocopy	retro_cjac_2779 ,
Dipodomys ordii	ENSDORG00000006822	1 retrocopy	retro_dord_612,
Erinaceus europaeus	ENSEEUG00000014393	1 retrocopy	retro_eeur_21,
Latimeria chalumnae	ENSLACG00000014539	1 retrocopy	retro_lcha_56,
Mus musculus	ENSMUSG00000040596	1 retrocopy	retro_mmus_2572,
Otolemur garnettii	ENSOGAG00000007615	1 retrocopy	retro_ogar_2784,
Tarsius syrichta	ENSTSYG00000011078	1 retrocopy	retro_tsyr_1983,