RetrogeneDB ID: retro_cjac_3903

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286214.1:34877..35231(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022619
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP1S3
• Ensembl ID: ENSCJAG00000012352
• Aliases: None
• Description: adaptor-related protein complex 1, sigma 3 subunit [Source:HGNC Symbol;Acc:18971]

Sequence

>retro_cjac_3903
AAAAAGATCACCAGAGAACTTGTTCAGACCGTTTTAGCACGGAAACCTAAAATGTGCAGCTTCCTTGAGTGGCGAGATCT
GAAGATTGTTTACAAAAGATGTGCTAGTCTGTATTTTTGCTGTGCTATTGAGGATCAGGACAATGAACTAATTACCCTGG
AAATAATTCATCGTTATGTGAAATTACTTGACAAGTATTTTGGCAGTACCTGTGAACTAGATATCATCTTTAATTTTGAG
AAGGCTTATTTTATTTTGGATGAGTTTCTTTTGGGAGGGGAAGTTCAGGAAACATCCAAGAAAAATGTCCTTAAAGCAAT
TGAGCAGGCCGATCTACTGCAGGAGGAAGCTGAA

Alignment

ORF - retro_cjac_3903 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.19 %
• Parental protein coverage: 76.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKITREIVQIILSRGHRTSSFIDWKELKLVYKRYASLYFCCAVDNQDNELLTLEIVHRYVELLDKYFGNV
          KKITRE.VQ..L.R.....SF..W..LK.VYKR.ASLYFCCA...QDNEL.TLEI.HRYV.LLDKYFG..
Retrocopy KKITRELVQTVLARKPKMCSFLEWRDLKIVYKRCASLYFCCAIEDQDNELITLEIIHRYVKLLDKYFGST

Parental  CELDIIFNFEKAYFILDEFIIGGEIQETSKKIAVKAIEDSDMLQETLE
          CELDIIFNFEKAYFILDEF..GGE.QETSKK...KAIE..D.LQE..E
Retrocopy CELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLLQEEAE

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	2.00 RPM
SRP051959_heart	0.04 RPM	0.16 RPM
SRP051959_kidney	0.02 RPM	4.75 RPM
SRP051959_liver	0.02 RPM	1.10 RPM
SRP051959_lung	0.20 RPM	0.41 RPM
SRP051959_lymph_node	0.09 RPM	0.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.04 RPM
SRP051959_spleen	0.27 RPM	0.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3903 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3903 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011939	5 retrocopies	retro_chof_113, retro_chof_1230, retro_chof_1299, retro_chof_1949, retro_chof_2099,
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 ,
Macropus eugenii	ENSMEUG00000016580	11 retrocopies	retro_meug_1074, retro_meug_1342, retro_meug_1488, retro_meug_168, retro_meug_1864, retro_meug_289, retro_meug_318, retro_meug_361, retro_meug_816, retro_meug_909, retro_meug_938,
Microcebus murinus	ENSMICG00000014406	1 retrocopy	retro_mmur_1492,
Monodelphis domestica	ENSMODG00000021198	1 retrocopy	retro_mdom_1427,
Mus musculus	ENSMUSG00000054702	3 retrocopies	retro_mmus_2202, retro_mmus_2799, retro_mmus_487,
Ochotona princeps	ENSOPRG00000013358	1 retrocopy	retro_opri_443,
Pan troglodytes	ENSPTRG00000012979	1 retrocopy	retro_ptro_2258,
Sarcophilus harrisii	ENSSHAG00000010973	1 retrocopy	retro_shar_695,