RetrogeneDB ID: retro_cjac_4162

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:47974728..47975839(-)
• Located in intron of: ENSCJAG00000002889

Retrocopy information

• Ensembl ID: ENSCJAG00000002911
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSCJAG00000001437
• Aliases: None
• Description: None

Sequence

>retro_cjac_4162
ATGTCGCACCCGTCCCCCCAAGCCAAGCCCTCCAACCCCAGTAACCCTCGAGTCTTCTTTGACGTGGACATCGGAGGGGA
GCGAGTGGGTCGAACTGTCTTAGAATTGTTTGCAGATATTGTGCCCAAAACTGCGGAAAATTTTCGTGCACTGTGTACAG
GAGAAAAAGGCATTGAACCCACAACTGGAAAACCTCTCCATTTCAAAGGATGCCCTTTTCATCAAATTATTAAGAAATTT
ATGATCCAGGGCGGAGACTTCTCAAATCGGAATGCGACAGGTGGAGAAAGTATTTACGGTGGAAAATTTGAAGATGAAAA
TTTCCATTATAAGCATGATCGGGAGGGTTTACTGAGCATGGCAAATGCAGGCCGCAACACAAATGGTTCTCAGTTTTTTA
TCACAATAGTTCCAACTCCTCATTTGGATGGGAAACATGTGGTGTTTGGCCAAGTAATTAAAGGAATAGGGGTGGTAAGG
ATATTGGAAAACGTAGAAGTGAAAGGTGAAAAACCTGCCAAATTGTGCGTTATTGCAGAATGTGGAGAATTGAAGGAAGG
AGATGATTGGGGAATATTCCCAAAAGATGGCTCTGGCGACAGTCATCCAGATTTCCCTGAGGATGTGGATATAGATTTAA
AAGACGTAGATAAAATTTTATTAATAACAGAAGACTTAAAAAACATTGGAAATACTTTTTTCAAATCCCAGAACTGGGAG
ATGGCCATTAAAAAATATGCAAAAGTTTTTAAGATATGTTGACAGTTCAAAGGCTGTTATCAAGACAGCAGATAGAGCCA
AGCTGCAACCTATAGCTTTAAGCTGTGTACTGAATATTGGTGCTTGTAAACTGAAGATGTCAAATTGGCAGGAAGCAATT
GACAGTTGTCTGGAGGCTCTTGAAATAGACCCATCAAATACCAAAGCATTGTACCAAAGAGCTCAAGGATGGCAAGGATT
AAGAGAATATGATCAAGCATTGGCTGATCTTAAAAAAGCTCAGGAGATAGCACCAGAAGATAAAGCTATCCAGGCAGAAT
TGCTGACAGTCAAACAAAAGATAAAGGCACAGAAAGATAAAGAGAAGGCAGCATATGCAAAAATGTTTGCT

Alignment

ORF - retro_cjac_4162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHPSPQAKPSNPSNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKG
          MSHPSPQAKPSNPSNPRVFFDVDIGGERVGR.VLELFADIVPKTAENFRALCTGEKGI.PTTGKPLHFKG
Retrocopy MSHPSPQAKPSNPSNPRVFFDVDIGGERVGRTVLELFADIVPKTAENFRALCTGEKGIEPTTGKPLHFKG

Parental  CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGRNTNGSQFFITTVPTP
          CPFH.IIKKFMIQGGDFSN.N.TGGESIYG.KFEDENFHYKHDREGLLSMANAGRNTNGSQFFIT.VPTP
Retrocopy CPFHQIIKKFMIQGGDFSNRNATGGESIYGGKFEDENFHYKHDREGLLSMANAGRNTNGSQFFITIVPTP

Parental  HLDGKHVVFGQVIKGIGVARILENVEVKGEKPAKLCIIAECGELKEGDDWGIFPKDGSGDSHPDFPEDAD
          HLDGKHVVFGQVIKGIGV.RILENVEVKGEKPAKLC.IAECGELKEGDDWGIFPKDGSGDSHPDFPED.D
Retrocopy HLDGKHVVFGQVIKGIGVVRILENVEVKGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDFPEDVD

Parental  IDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKV-LRYVDSSKAVIETADRAKLQPIALSCVLNI
          IDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKV.LRYVDSSKAVI.TADRAKLQPIALSCVLNI
Retrocopy IDLKDVDKILLITEDLKNIGNTFFKSQNWEMAIKKYAKV>LRYVDSSKAVIKTADRAKLQPIALSCVLNI

Parental  GACKLKMSNWQEAIDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLK
          GACKLKMSNWQEAIDSCLEALEIDPSNTKALY.RAQGWQGL.EYDQALADLKKAQEIAPEDKAIQAELL.
Retrocopy GACKLKMSNWQEAIDSCLEALEIDPSNTKALYQRAQGWQGLREYDQALADLKKAQEIAPEDKAIQAELLT

Parental  VKQKIKAQKDKEKAVYAKMFA
          VKQKIKAQKDKEKA.YAKMFA
Retrocopy VKQKIKAQKDKEKAAYAKMFA

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	0.16 RPM	20.06 RPM
SRP051959_heart	0.12 RPM	20.10 RPM
SRP051959_kidney	0.13 RPM	21.92 RPM
SRP051959_liver	0.17 RPM	28.79 RPM
SRP051959_lung	0.10 RPM	23.96 RPM
SRP051959_lymph_node	0.16 RPM	34.95 RPM
SRP051959_skeletal_muscle	0.13 RPM	34.70 RPM
SRP051959_spleen	0.08 RPM	29.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4162 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162 ,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,