RetrogeneDB ID: retro_cjac_2960

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:4245245..4245621(-)
• Located in intron of: ENSCJAG00000020506

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007120
• Aliases: None
• Description: None

Sequence

>retro_cjac_2960
GAGCGAAGCGGTGGGGAGCAGGCACAGGACTGGGATGCTGTGGCCCCCAAGAGGCCCTGAGTTGGGGCAGGAAACAAGAT
CGGAGGCTGTAGGCTTATTGTGGTGCTGGAAGGGGCCAGTCTGGAGACAGTCAAGGTAGGGAAGACACGTGAGCTACTCA
ACTGTGACAAGCACAAGTCTACATTGCTGAAGAATGGACGGGACCCCGGGGAAGGGCGGCCAGACATAGCCCACCAGTTT
ACTGATGCTGATGGAAAGTCCCCTGAACCGAGCTGGCTTGCTGCAAGTTTATATCCACAAACAGAAGAATGTTCTGATTG
AAGTGAACCCCCAGACCCGAATCCCCAGAACCTTTGACCGCTTTTGTGGCCTCGTG

Alignment

ORF - retro_cjac_2960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 51.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERSCGEQLEDWDAVAPKRPRVGAGNKIGGRRLIVVLEGASLETVKVGKTYELLNCDKHKSILLKNGRDPG
          ERS.GEQ..DWDAVAPKRP.VGAGNKIGG.RLIVVLEGASLETVKVGKT.ELLNCDKHKS.LLKNGRDPG
Retrocopy ERSGGEQAQDWDAVAPKRP*VGAGNKIGGCRLIVVLEGASLETVKVGKTRELLNCDKHKSTLLKNGRDPG

Parental  EVRPDIAHQ-SLLMLMDSPLNRAGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLM
          E.RPDIAHQ..L.....SPLNRAGLLQVYIH.QKNVLIEVNPQTRIPRTFDRFCGL.
Retrocopy EGRPDIAHQ>LLMLM-ESPLNRAGLLQVYIHKQKNVLIEVNPQTRIPRTFDRFCGLV

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	0.58 RPM	5.70 RPM
SRP051959_heart	0.30 RPM	7.45 RPM
SRP051959_kidney	0.29 RPM	8.03 RPM
SRP051959_liver	0.35 RPM	7.19 RPM
SRP051959_lung	0.44 RPM	6.73 RPM
SRP051959_lymph_node	0.59 RPM	8.49 RPM
SRP051959_skeletal_muscle	0.22 RPM	10.05 RPM
SRP051959_spleen	0.34 RPM	7.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2960 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013753	1 retrocopy	retro_amel_1924,
Callithrix jacchus	ENSCJAG00000007120	1 retrocopy	retro_cjac_2960 ,
Gorilla gorilla	ENSGGOG00000004287	1 retrocopy	retro_ggor_3077,
Macropus eugenii	ENSMEUG00000000831	1 retrocopy	retro_meug_1299,
Myotis lucifugus	ENSMLUG00000009196	1 retrocopy	retro_mluc_737,
Macaca mulatta	ENSMMUG00000010207	1 retrocopy	retro_mmul_671,
Nomascus leucogenys	ENSNLEG00000005080	1 retrocopy	retro_nleu_501,
Otolemur garnettii	ENSOGAG00000006975	2 retrocopies	retro_ogar_2971, retro_ogar_945,
Pongo abelii	ENSPPYG00000004215	1 retrocopy	retro_pabe_2924,
Rattus norvegicus	ENSRNOG00000012828	1 retrocopy	retro_rnor_1459,