RetrogeneDB ID: retro_cjac_2423

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:31822606..31823056(-)
• Located in intron of: ENSCJAG00000003246

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019647
• Aliases: None
• Description: None

Sequence

>retro_cjac_2423
AAACACGACTGCAAGTCATTGGACCCTGAGCAGGAGACTCTAACCAACATGCTGCCTCCATGTGGACTCCAGCCCACAAG
GTCACTTTTCAATAGGATGGACTTTGAAGACTTGGGGTTGGTAGTAGATTGGGACCACCACCTGCCTCCACCAGCTGCCA
AGACTGTTGTTGAGAACCTCCCCAGGATAGTCATCAGAGGCTCTCAGGCTAAGCTCAAGTGCCCCATGTGTCTTTTGGAA
TTTGAGGAAGAGGAGATTGCCATTGAGATGACTTGCCATCACCTCTTCCATTCCAGTTGCATTCTGCCCTGGCTAAGCAA
GACAAATTCCTGTCCCCAGTGCCACCATGAGCTGCTCATTGATGGTGACACTGAAGATGAGCAGAGATGAGATAACGCTC
AAAAACAGCAGCAGCAGCATCGACTGGAGAACCTTCAGGGAGCGATGTAC

Alignment

ORF - retro_cjac_2423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.33 %
• Parental protein coverage: 95.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EHDCEPLDPEQETRTNML----LELARSLFNRMDFEDLGLVVDWDHHLPPPAAKTVVENLPRTVIRGSQA
          .HDC..LDPEQET.TNML....L...RSLFNRMDFEDLGLVVDWDHHLPPPAAKTVVENLPR.VIRGSQA
Retrocopy KHDCKSLDPEQETLTNMLPPCGLQPTRSLFNRMDFEDLGLVVDWDHHLPPPAAKTVVENLPRIVIRGSQA

Parental  ELKCPVCLLEFEEEETAIEMPCHHLFHSSCILPWLSKTNSCPLCRHELPTDDDTYEEHRRDKARKQQQQH
          .LKCP.CLLEFEEEE.AIEM.CHHLFHSSCILPWLSKTNSCP.C.HEL..D.DT..E.R.D.A.KQQQQH
Retrocopy KLKCPMCLLEFEEEEIAIEMTCHHLFHSSCILPWLSKTNSCPQCHHELLIDGDTEDEQR*DNAQKQQQQH

Parental  RLENLHGAMY
          RLENL.GAMY
Retrocopy RLENLQGAMY

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	6.77 RPM
SRP051959_heart	0.00 RPM	8.05 RPM
SRP051959_kidney	0.00 RPM	20.34 RPM
SRP051959_liver	0.00 RPM	15.10 RPM
SRP051959_lung	0.00 RPM	10.18 RPM
SRP051959_lymph_node	0.00 RPM	9.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.63 RPM
SRP051959_spleen	0.00 RPM	8.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2423 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2423 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019647	3 retrocopies	retro_cjac_2423 , retro_cjac_355, retro_cjac_3849,
Homo sapiens	ENSG00000168894	3 retrocopies	retro_hsap_1005, retro_hsap_3771, retro_hsap_938,
Gorilla gorilla	ENSGGOG00000004953	3 retrocopies	retro_ggor_2537, retro_ggor_759, retro_ggor_799,
Macaca mulatta	ENSMMUG00000017824	3 retrocopies	retro_mmul_1128, retro_mmul_1637, retro_mmul_808,
Otolemur garnettii	ENSOGAG00000012284	1 retrocopy	retro_ogar_2742,
Pongo abelii	ENSPPYG00000012225	2 retrocopies	retro_pabe_3083, retro_pabe_807,
Pan troglodytes	ENSPTRG00000012138	2 retrocopies	retro_ptro_2557, retro_ptro_650,