RetrogeneDB ID: retro_cjac_2054

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:47875056..47875586(-)
• Located in intron of: ENSCJAG00000005608

Retrocopy information

• Ensembl ID: ENSCJAG00000005624
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2054
GCTCCTGCCAGCATGGCAACAGTAGTTCTAGGGGGAGACAGCAGGGGCCCTGAGGGTACCTTCCCCAATCAGACTGAGGA
ACGGGGGCCACATCAGGGTCCTTCAGAAGGCACTGTGGATTGGAGCCGTGAGGAGCCTGAGGAAGAACAGGAGGAAACGG
GGTCGGGCCCAGCTAGCTACTCCTACCAGCCCCTGAACCAGGATCCTGAACAAGAGGAGGTGGAGCTGGCACTAGTCGGG
GATGGAGATGTAGCTGCTGACATCCAGGATCGAATCCAGGCCCTGGGCCTTCATTTGCCAGACCCACCATTAGACAGTGA
AGATGAAGATGAGGAAGGACCTACAGCTTGAACAACCACAGCTCTCTTCTCATGGACCCAGAACAGGTAGAGCTGGTGAA
AAGGACCATGGCTGGAGTTAGCCTGCCTGTGCCAGGGGTTCCTGCCTGGGCTCGGGAGATACCAGATGCCCAGTGGGAAG
ACGCGGCACAGAAAGCCCTCCAAGCCCGGCAGGCATCCCCTGCCTGGAAG

Alignment

ORF - retro_cjac_2054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APARMATVVLGGDSMGPERIFPNQTEELGPHQGPSEGTGDWSSEEPEEEQEETGSGPASYSYQPLNQDPE
          APA.MATVVLGGDS.GPE..FPNQTEE.GPHQGPSEGT.DWS.EEPEEEQEETGSGPASYSYQPLNQDPE
Retrocopy APASMATVVLGGDSRGPEGTFPNQTEERGPHQGPSEGTVDWSREEPEEEQEETGSGPASYSYQPLNQDPE

Parental  QEEVELAPVGDGDVVADIQDRIQALGLHLPDPPLESDDEDEEGATA-LNNHSSIPMDPEHVELVKRTMAG
          QEEVELA.VGDGDV.ADIQDRIQALGLHLPDPPL.S.DEDEEG.TA.LNNHSS..MDPE.VELVKRTMAG
Retrocopy QEEVELALVGDGDVAADIQDRIQALGLHLPDPPLDSEDEDEEGPTA<LNNHSSLLMDPEQVELVKRTMAG

Parental  VSLPAPGVPAWAREISDAQWEDVVQKALQARQASPAWK
          VSLP.PGVPAWAREI.DAQWED..QKALQARQASPAWK
Retrocopy VSLPVPGVPAWAREIPDAQWEDAAQKALQARQASPAWK

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	1.13 RPM	9.61 RPM
SRP051959_heart	0.91 RPM	9.00 RPM
SRP051959_kidney	1.04 RPM	16.17 RPM
SRP051959_liver	0.56 RPM	13.65 RPM
SRP051959_lung	1.59 RPM	12.35 RPM
SRP051959_lymph_node	2.26 RPM	11.14 RPM
SRP051959_skeletal_muscle	0.44 RPM	8.04 RPM
SRP051959_spleen	1.43 RPM	12.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2054 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2054 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2054 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,