RetrogeneDB ID: retro_cjac_2742

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:84937934..84938366(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022852
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSCJAG00000005786
• Aliases: None
• Description: adaptor-related protein complex 4, sigma 1 subunit [Source:HGNC Symbol;Acc:575]

Sequence

>retro_cjac_2742
ATGATAAAATTTTTCCTCATGGTGAATAAACAAGGGCAGACTCGACTTTCTAAGTACTATGAACATGTGGATATTAATAA
GCATACGTTTCTGGAAACAGAAGTCATAAAGAGCTGTCTCTCTCGATCCAATGAACAATGCTCTTTCATTGAATATAAGG
ATTTTAAGTTGATATATTGGCAGTATGCAGCTCTCTTCATTGTGGTTGGAGTTAATGACACTGAGAACGAGATGGCTATT
TATGAATTCATTCATAACTTTGTGGAAGTTTTAGATGAATATTTCAGCCGAGTGAGTGAATTAGATATAATGTTTAATTT
AGATAAAGTACACATCATTTTGGATGAGATGGTGTTAAATGGCTGCATTGTGGAAACTAACAGGGCAAGAATTCTTGCCC
CTCTACTAATTCTTGATAAGATGTCAGAAAGC

Alignment

ORF - retro_cjac_2742 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIKFFLMVNKQGQTRLSKYYEHVDINKRTFLETEVIKSCLSRSNEQCSFIEYKDFKLIYRQYAALFIVVG
          MIKFFLMVNKQGQTRLSKYYEHVDINK.TFLETEVIKSCLSRSNEQCSFIEYKDFKLIY.QYAALFIVVG
Retrocopy MIKFFLMVNKQGQTRLSKYYEHVDINKHTFLETEVIKSCLSRSNEQCSFIEYKDFKLIYWQYAALFIVVG

Parental  VNDTENEMAIYEFIHNFVEVLDEYFSRVSELDIMFNLDKVHIILDEMVLNGCIVETNRARILAPLLILDK
          VNDTENEMAIYEFIHNFVEVLDEYFSRVSELDIMFNLDKVHIILDEMVLNGCIVETNRARILAPLLILDK
Retrocopy VNDTENEMAIYEFIHNFVEVLDEYFSRVSELDIMFNLDKVHIILDEMVLNGCIVETNRARILAPLLILDK

Parental  MSES
          MSES
Retrocopy MSES

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	0.22 RPM	2.64 RPM
SRP051959_heart	0.35 RPM	5.88 RPM
SRP051959_kidney	0.27 RPM	4.17 RPM
SRP051959_liver	0.26 RPM	2.25 RPM
SRP051959_lung	0.26 RPM	4.49 RPM
SRP051959_lymph_node	0.55 RPM	4.61 RPM
SRP051959_skeletal_muscle	1.31 RPM	13.71 RPM
SRP051959_spleen	0.29 RPM	4.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2742 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2742 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312,
Callithrix jacchus	ENSCJAG00000005786	1 retrocopy	retro_cjac_2742 ,
Callithrix jacchus	ENSCJAG00000012352	2 retrocopies	retro_cjac_3187, retro_cjac_3903,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889,