RetrogeneDB ID: retro_cjac_2845

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:117062563..117063622(-)
• Located in intron of: ENSCJAG00000004698

Retrocopy information

• Ensembl ID: ENSCJAG00000035086
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003979
• Aliases: None
• Description: None

Sequence

>retro_cjac_2845
ATGATGGCTCAGGCAAATATGCTCCCCGTGGCTGATGTGTTGAGTCAAGATGAACTGCGCAAAAAGCTATACCAGACATT
TAAGGATCGGGGTATACTGGACACACTCAATACACAACTTCGAAACCAGCTAATTCATGAGCTGATGCATCCTGTATCTA
GTGGAGAACTGCAACCTCGGTCCATTTCAGTGGAAGGGAGCTCCCTCTTAATAGGCGCCTCTAACTCTTTAGTGGCAGAT
CACTTACAAAGATGTGGCTATGAATATTCACTTTCTGTTTTCTTTCCAGAAAGTGGTTTGGCAAAAGGAAAGGTATTTAC
TATGCGGGATCTATTACAACTCATGAAAATCAACCCTATTTCCAGTCTCTACAAATCACTGGTTTCAGGATCTGATAAAG
AAAACCATAAAGGTTTTCTTATGCATTTTTTAAAAGAATTGGCAGAATATCATCAAGCTAAAGAGAGTTGTAATATGGAA
ACTCAGACAAGTTCGACATTTAGCAGAGATTTTCTGGCTGAGAAGCTTCAGCTTATTGATGATCAATTTGCAGATGCTTT
CCCTCAGCGTATCAAATTCGAGTCTTTAGAAATAAAGCTAAATGAATATAAGAGAGAAATAGAAGAGCAACTTCAGGCAG
AAATGGGACAAAAGTTGAAGTTTTTTAAAGATACTGAGATAGCAAAAATTAAAATGGAAGTGAGAAAAAAGTATGAGAAG
GAATTAGCCATATTCCAGAATGATTTTGAGAAAGCTTGTCAAGCAAAATCTGAAGCCCTCATTCTTAGGGAAAAGAGCAC
CCTTGAGAGAATTCAAAAGCACCAAGAGATTGAAACAAAAGAAATTTATGCTCAACGGCAACTTTTACTAAAAGATATGG
ATTTACTAAGAAGAAGAGAAGCAGAGCTGAAGCAAAGAGTTGAAGCTTTTGAATTGAACCAGAAACTCCAGGAAGAAAAA
CATAAAAGCATGACTGAGGCACTCCAGAGACGGGAGCAGAATATAAAGAGTTTTGAGGAGACCTATGACCAAAAGCTCAA
GAATGAACTTCTAAAGTAT

Alignment

ORF - retro_cjac_2845 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.35 %
• Parental protein coverage: 96.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMAQSNMLPVADVLSQDELRKKLYQTFKDRGILDTLKTQLRNQLIHELMHPVLSGELQPRSISVEGSSLF
          MMAQ.NMLPVADVLSQDELRKKLYQTFKDRGILDTL.TQLRNQLIHELMHPV.SGELQPRSISVEGSSL.
Retrocopy MMAQANMLPVADVLSQDELRKKLYQTFKDRGILDTLNTQLRNQLIHELMHPVSSGELQPRSISVEGSSLL

Parental  IGASNSLVADHLQRCGYEYSLSVFFPESGLAKEKVFTMQDLLQLIKINPTSSLYKSLVSGSDKDNQKGFL
          IGASNSLVADHLQRCGYEYSLSVFFPESGLAK.KVFTM.DLLQL.KINP.SSLYKSLVSGSDK.N.KGFL
Retrocopy IGASNSLVADHLQRCGYEYSLSVFFPESGLAKGKVFTMRDLLQLMKINPISSLYKSLVSGSDKENHKGFL

Parental  MHFLKELAEYHQAKEGCNMETQTSSIFSRDSLAEKLQLIDDQFADAYPQRVKFESLEIKLNEYKREIEEQ
          MHFLKELAEYHQAKE.CNMETQTSS.FSRD.LAEKLQLIDDQFADA.PQR.KFESLEIKLNEYKREIEEQ
Retrocopy MHFLKELAEYHQAKESCNMETQTSSTFSRDFLAEKLQLIDDQFADAFPQRIKFESLEIKLNEYKREIEEQ

Parental  LRAEMCQKLKIFKDTEIAKIKMEAKKKYEKELAMFQNDFEKACQAKSEALILREKSTLERIQKHQEIETK
          L.AEM.QKLK.FKDTEIAKIKME..KKYEKELA.FQNDFEKACQAKSEALILREKSTLERIQKHQEIETK
Retrocopy LQAEMGQKLKFFKDTEIAKIKMEVRKKYEKELAIFQNDFEKACQAKSEALILREKSTLERIQKHQEIETK

Parental  EIYAQRQLLLKDMDLLRGREAELKQRVEAFELHQKLQEEKHKSVTEALRRREQNIKSFEETYDQKLKNEL
          EIYAQRQLLLKDMDLLR.REAELKQRVEAFEL.QKLQEEKHKS.TEAL.RREQNIKSFEETYDQKLKNEL
Retrocopy EIYAQRQLLLKDMDLLRRREAELKQRVEAFELNQKLQEEKHKSMTEALQRREQNIKSFEETYDQKLKNEL

Parental  LNF
          L..
Retrocopy LKY

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	0.00 RPM	9.52 RPM
SRP051959_heart	0.11 RPM	8.84 RPM
SRP051959_kidney	0.00 RPM	12.38 RPM
SRP051959_liver	0.00 RPM	5.76 RPM
SRP051959_lung	0.02 RPM	12.92 RPM
SRP051959_lymph_node	0.02 RPM	13.01 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.88 RPM
SRP051959_spleen	0.02 RPM	11.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2845 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2845 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003979	1 retrocopy	retro_cjac_2845 ,
Homo sapiens	ENSG00000046651	1 retrocopy	retro_hsap_3164,
Gorilla gorilla	ENSGGOG00000006453	1 retrocopy	retro_ggor_1352,
Nomascus leucogenys	ENSNLEG00000009180	1 retrocopy	retro_nleu_2496,
Pan troglodytes	ENSPTRG00000021675	1 retrocopy	retro_ptro_2274,