RetrogeneDB ID: retro_cjac_1338

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:46833960..46835216(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013247
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSCJAG00000020963
• Aliases: None
• Description: None

Sequence

>retro_cjac_1338
ATGGCGACCTCTCCGGGTTCCAACACCTACAACAGGCAGAACTGGGAAGATGCGGACTTCCCCATTCTGTGCCAGACATG
TCTTGGAGAAAACCCATATATCCGAATGACCAAAGAAAAGTATGGGAAGGAATGCAAAATCTGTGCCAGGCCATTCACAA
TGTTTCGCTGGTGCCCCGGAGTCCGTATGCGTTTCAAGAAGACTGAAGTGTGCCAGACCTGCAGTAAATTGAAGAATGTC
TGTCAGACCTGCCTCTTAGACCTAGAGTATGGCCTGCCCATCCAGGTTCGTGATGCAGGATTGTCTTTTAAAGATGACAT
GCCAAAGTCAGATGTCAACAAAGAGTACTATACACAGAATATGGAGAGAGAGATTTCTAACTCTGATGGAACACGGCCAG
TTGGCATGCTGGGGAAAGCCACATCTACCAGTGACATGCTGCTCAAACTGGCCCGGACCACACCCTACTACAAAAGGAAT
CGACCCCACATTTGCTCCTTCTGGGTGAAAGGAGAGTGTAAGAGAGGAGAGGAATGTCCATACAGACATGAGAAGCCTAC
AGATCCAGATGACCCCCTTGCTGATCAGAATATTAAAGATCGATACTACGGAATCAATGATCCTGTAGCTGACAAGCTTC
TAAAGCAGGCTTCGACAATGCCTCGGCTGGACCCACCAGAGGATAAAACTATCACCACACTATATGTTGGTGGTCTGGGT
GATACTATTACTGAGACAGATTTAAGAAATCACTTCTACCAGTTTGGAGAGATCCGGACGATCACTGTTGTGCAAAGACA
GCAGTGTGCTTTCATCCAGTTTGCCACGAGGCAGGCTGCAGAAGTGGCTGCTGAGAAGTCCTTTAATAAGTTGATTGTAA
ATGACCGCAGACTGAATGTGAAATGGGGAAGATCCCAAGCAGCCAGAGGAAAAGAAAAAGAGAAAGATGGAACCACAGAC
TCTGGGATCAAACTGGAACCAGTTCCAGGATTGCCAGGAGCTCTTCCTCCTCCTCCTGCGGCAGAAGAAGCCTCTGCCAA
CTACTTCAACTTGCCCCCAAGTGGTCCTCCAGCTGTGGTGAACATTGCCCTGCCACCACCCCCTGGTATCGCCCCACCCC
CCGACCAGGTTTTGGGTCACACATATTCCACCCAATGGGACCACCCCCTCCTTTCATGAGGGCTCCAGGACCAATCCACT
ATCCTTCTCAGGACCCTCAGCGGATGGGAGCTCATGCTGGAAAACACAGCAGTCCC

Alignment

ORF - retro_cjac_1338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRKTKEKYGKECKICARPFTVFRWCPGVRMRFKKTEV
          MATS.GSNTYNRQNWEDADFPILCQTCLGENPYIR.TKEKYGKECKICARPFT.FRWCPGVRMRFKKTEV
Retrocopy MATSPGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTMFRWCPGVRMRFKKTEV

Parental  CQTCSKLKNVCQTCLLDLEYAGLPIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGK
          CQTCSKLKNVCQTCLLDLEY.GLPIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGK
Retrocopy CQTCSKLKNVCQTCLLDLEY-GLPIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGK

Parental  ATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPV
          ATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPV
Retrocopy ATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPV

Parental  ADKLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQA
          ADKLLK.ASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQA
Retrocopy ADKLLKQASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQA

Parental  AEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEASANY
          AEVAAEKSFNKLIVN.RRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAA.EEASANY
Retrocopy AEVAAEKSFNKLIVNDRRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAA-EEASANY

Parental  FNLPPSGPPAVVNIALPPPPGIAPPPP-PGFGSHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS
          FNLPPSGPPAVVNIALPPPPGIAPPP..PGFGSH.FHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS
Retrocopy FNLPPSGPPAVVNIALPPPPGIAPPPD<PGFGSHIFHPMGPPPPFMRAPGPIHYPSQDPQRMGAHAGKHS

Parental  SP
          SP
Retrocopy SP

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	0.89 RPM	5.95 RPM
SRP051959_heart	0.86 RPM	5.68 RPM
SRP051959_kidney	1.20 RPM	7.10 RPM
SRP051959_liver	0.56 RPM	5.33 RPM
SRP051959_lung	1.07 RPM	9.08 RPM
SRP051959_lymph_node	1.46 RPM	11.03 RPM
SRP051959_skeletal_muscle	1.20 RPM	8.23 RPM
SRP051959_spleen	1.28 RPM	9.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1338 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338 , retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Otolemur garnettii	ENSOGAG00000011086	1 retrocopy	retro_ogar_2206,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,