RetrogeneDB ID: retro_cjac_3999

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286888.1:747..1434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF141
• Ensembl ID: ENSCJAG00000011014
• Aliases: None
• Description: ring finger protein 141 [Source:HGNC Symbol;Acc:21159]

Sequence

>retro_cjac_3999
ATGGGACAGCAAATTTCGGATCAGACACAGTTGGTTATTAGCAAGTTACCAGAAAAAGTAGCAAAACATGTCACATTGGT
TCGAGAAAATGGCTCCTTAACTTACAAAGAACTTTTTGGGAGAGTAGCTGAGCTTAATGATGTAACTGCTAAAGTGGCTT
CTGGCCAGGAAAAACGTCTCTTTGAGGTACAACCTGGGTCTGATTCCTCTGCTTTTTGGAAAGTGGTGGTACGGGTGGTC
TGCATCAAGATTAACAAAAGCAGTGGCATTGTGGAGGCATCACGGATCATGAATTTGTACCAGTTTATTCAAATTTATAA
AGATATCACAAGTCAAGCAGCAGGAGCATTAGCACAAAGCTCCACCTCTGAAGAACCTGATGAAAGCTCATCCTCTGTAA
CATCTTGTCAGGCTAGTTTTTGGATTGGAAGGGTAAAGCAGCTGACTGATGAGGAGGAGTGTTGTATCTGTATGGACTGG
CAAGCTGACCTCATCCTGCCTTGTGCTCACAGCTTTTGTCAGAAGTGTATTGATAAATGGAGTGATTGACACAGGAATTG
CCCTATTTGTTGCCTACAGATGACTGGAGCAAATGAATTTTGGGTGGTATCAGATGCACCCACTGAAGATGATATAGCTA
ACTATGTTCTTAACATGGCTGACGAGGCAGGCCAGCCCCACAGGCCA

Alignment

ORF - retro_cjac_3999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGQQISDQTQLVISKLPEKVAKHVTLVRESGSLTYEEFLGRVAELNDVTAKVASGQEKHLLFEVQPGSDS
          MGQQISDQTQLVISKLPEKVAKHVTLVRE.GSLTY.E..GRVAELNDVTAKVASGQEK..LFEVQPGSDS
Retrocopy MGQQISDQTQLVISKLPEKVAKHVTLVRENGSLTYKELFGRVAELNDVTAKVASGQEKR-LFEVQPGSDS

Parental  SAFWKVVVRVVCTKINKSSGIVEASRIMNLYQFIQLYKDITSQAAGVLAQTSTSEEPDESSSSVTSCQAS
          SAFWKVVVRVVC.KINKSSGIVEASRIMNLYQFIQ.YKDITSQAAG.LAQ.STSEEPDESSSSVTSCQAS
Retrocopy SAFWKVVVRVVCIKINKSSGIVEASRIMNLYQFIQIYKDITSQAAGALAQSSTSEEPDESSSSVTSCQAS

Parental  FWMGRVKQLTDEEECCICMDGRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESWVVSDAPTE
          FW.GRVKQLTDEEECCICMD..ADLILPCAHSFCQKCIDKWSD.HRNCPIC.LQMTGANE.WVVSDAPTE
Retrocopy FWIGRVKQLTDEEECCICMDWQADLILPCAHSFCQKCIDKWSD*HRNCPICCLQMTGANEFWVVSDAPTE

Parental  DDMANYILNMADEAGQPHRP
          DD.ANY.LNMADEAGQPHRP
Retrocopy DDIANYVLNMADEAGQPHRP

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	0.31 RPM	19.28 RPM
SRP051959_heart	0.68 RPM	19.63 RPM
SRP051959_kidney	0.47 RPM	28.15 RPM
SRP051959_liver	0.24 RPM	19.08 RPM
SRP051959_lung	0.76 RPM	23.82 RPM
SRP051959_lymph_node	0.14 RPM	12.05 RPM
SRP051959_skeletal_muscle	0.13 RPM	20.42 RPM
SRP051959_spleen	0.42 RPM	18.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3999 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3999 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011014	1 retrocopy	retro_cjac_3999 ,
Cavia porcellus	ENSCPOG00000007808	2 retrocopies	retro_cpor_175, retro_cpor_198,
Macropus eugenii	ENSMEUG00000014558	1 retrocopy	retro_meug_1251,
Mus musculus	ENSMUSG00000030788	1 retrocopy	retro_mmus_2996,
Oryctolagus cuniculus	ENSOCUG00000002807	1 retrocopy	retro_ocun_1507,
Otolemur garnettii	ENSOGAG00000001765	1 retrocopy	retro_ogar_1262,
Sarcophilus harrisii	ENSSHAG00000002101	2 retrocopies	retro_shar_148, retro_shar_694,
Ictidomys tridecemlineatus	ENSSTOG00000019740	1 retrocopy	retro_itri_1573,