RetrogeneDB ID: retro_cjac_824

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:9280719..9281233(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEA1
• Ensembl ID: ENSCJAG00000004894
• Aliases: None
• Description: male-enhanced antigen 1 [Source:HGNC Symbol;Acc:6986]

Sequence

>retro_cjac_824
CCTGCATGGATGGCAAAAGTAGTTTTAGGGTAGGATAGCATGGGCCCTGAGTGTATCTTCCCCAATCTGACTGAGGAACT
GGGGCCACATCGGGGCCCTTCAGAAGGCACTGGGAATTGGAGCAGTGAGGAGCCTGAGGAAGAACAGGAGGAAACAGGGG
TCGGGCCCAGCTAGCTACTCCTACCAGCCCCTGAACCAAGATCCTGAACAAGAGGAGGTGGAGCTGGCACCAGTTGGGGA
TGGAGATGTAGTTGCTGACATCCAGGATTGAATCCAAGCTCTGGGGCTTCATTTGTCAGACTCACCATTAGAGAGTGAAG
ATGAAGATGAGGAAGGAGCTACCGTGCTGAACAACCACAGCTCCATTCCCATGGACCCAGAACATGTAGAGCTGGTGAAA
AGAACAATGGCTGGAGTAAGCCTGCCTGCGCCAGGGGTTCCTGCCTGGCTTGGGAGATTATCAGATGCCCAGTGGGAAGA
TGTGGTACAGAAAGCCCTCCAAGCCCGGCAGGCA

Alignment

ORF - retro_cjac_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.12 %
• Parental protein coverage: 96.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PARMATVVLGGDSMGPERIFPNQTEELGPHQGPSEGTGDWSSEEPEEEQEET-GSGPASYSYQPLNQDPE
          PA.MA.VVLG.DSMGPE.IFPN.TEELGPH.GPSEGTG.WSSEEPEEEQEET.GSGPASYSYQPLNQDPE
Retrocopy PAWMAKVVLG*DSMGPECIFPNLTEELGPHRGPSEGTGNWSSEEPEEEQEET>GSGPASYSYQPLNQDPE

Parental  QEEVELAPVGDGDVVADIQDRIQALGLHLPDPPLESDDEDEEGATALNNHSSIPMDPEHVELVKRTMAGV
          QEEVELAPVGDGDVVADIQD.IQALGLHL.D.PLES.DEDEEGAT.LNNHSSIPMDPEHVELVKRTMAGV
Retrocopy QEEVELAPVGDGDVVADIQD*IQALGLHLSDSPLESEDEDEEGATVLNNHSSIPMDPEHVELVKRTMAGV

Parental  SLPAPGVPAWAREISDAQWEDVVQKALQARQA
          SLPAPGVPAW....SDAQWEDVVQKALQARQA
Retrocopy SLPAPGVPAWLGRLSDAQWEDVVQKALQARQA

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	0.07 RPM	9.61 RPM
SRP051959_heart	1.46 RPM	9.00 RPM
SRP051959_kidney	0.18 RPM	16.17 RPM
SRP051959_liver	2.64 RPM	13.65 RPM
SRP051959_lung	0.15 RPM	12.35 RPM
SRP051959_lymph_node	0.09 RPM	11.14 RPM
SRP051959_skeletal_muscle	0.04 RPM	8.04 RPM
SRP051959_spleen	0.15 RPM	12.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_824 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_824 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012655	1 retrocopy	retro_amel_1620,
Bos taurus	ENSBTAG00000005536	1 retrocopy	retro_btau_240,
Canis familiaris	ENSCAFG00000001756	1 retrocopy	retro_cfam_1643,
Callithrix jacchus	ENSCJAG00000004894	2 retrocopies	retro_cjac_2054, retro_cjac_824 ,
Cavia porcellus	ENSCPOG00000022111	1 retrocopy	retro_cpor_1530,
Echinops telfairi	ENSETEG00000002439	1 retrocopy	retro_etel_236,
Felis catus	ENSFCAG00000031337	1 retrocopy	retro_fcat_1772,
Loxodonta africana	ENSLAFG00000013881	1 retrocopy	retro_lafr_60,
Myotis lucifugus	ENSMLUG00000012138	2 retrocopies	retro_mluc_1819, retro_mluc_851,
Monodelphis domestica	ENSMODG00000019002	1 retrocopy	retro_mdom_878,
Oryctolagus cuniculus	ENSOCUG00000001565	2 retrocopies	retro_ocun_1312, retro_ocun_1446,
Pelodiscus sinensis	ENSPSIG00000002330	1 retrocopy	retro_psin_56,
Pteropus vampyrus	ENSPVAG00000008711	1 retrocopy	retro_pvam_266,
Rattus norvegicus	ENSRNOG00000017144	2 retrocopies	retro_rnor_716, retro_rnor_961,
Tupaia belangeri	ENSTBEG00000012294	2 retrocopies	retro_tbel_1462, retro_tbel_3528,
Tursiops truncatus	ENSTTRG00000006996	1 retrocopy	retro_ttru_357,