RetrogeneDB ID: retro_cjac_2963

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:11013272..11014346(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPIL4
• Ensembl ID: ENSCJAG00000019613
• Aliases: None
• Description: None

Sequence

>retro_cjac_2963
ATAATTAAGAAAATTAATGAGACCTTTGTTGACAAAGACTTTGTACCATATTAGGATATCAGGATAAATCACACGGTGAT
TTTAGATGATCCATTTGATGACCCTCCTGATTTATTAATCCCTGATCGATCACCAGAACCTACAAGGGAACAATTAGATA
GTGGTCGAATAGGAGCAGATGAAGAAATTGATGATTTCAAAGGATGATCAGCTGAGGAAGTTCGAAGAAATAAAGGCAGA
AAAAGAGGCTAAAACTCAGGCTATACTTTTAGAGATGGTGGGAGACCTACCTGATGCAGATATTAAACCTCCAGAAAATG
TGTTGTTTGTGTGTAAATTGAACCCAGTGACCACAGATGAGGATCTGGAAATAATATTCTCTAGATTTGGGCCAATAAGA
AGTTGTGAAGTTATCCGGGACTGGAAGACAGGAGAGTCCCTCTGTTACGCTTTTATTGAATTTGAAAAGGAAGAAGATTG
TGAGAAAGCATTCTTCAAAATGGACAATGTACTTATAGATGACAGAAGAATACATGTGGATTTTAGCCAGTCTGTTGCAA
AGGTTAAATTGAAAGGAAAAGGTGAGAAATACACCAAGAGTGATTTCAAGGAATATGAAAAAGAACAAAATAATCCATCT
AATTTGGTTCTGAAAGATAAAGTAAAGCCCAAACAGGATGCAAAATACGATCTTATGCTAGATGAGCAGGCAGAAGACTC
AAAATCAAGTCACGCACACACAAGTAAAAAACACGAGAAGAAAACCCGTCACTGCTCTGAAGAAAAAGAAGATGAGGACT
ACATGCCAATCAAAAATCCTAATCAGGATATCTATAGAGAAATGGGGTTTGGTCACTATGAAGAAGAAGAAAGCTGTTGG
GAGAAACAAAAGAGTGAAAAGAGAGACCGAACTCAGAACCGAAGTCGTAGCTGATCTCAAGAGAGGGATGGCCATCATAG
TAATAGTCACAAATCCAAATCCAAACAGATCTTTACGAAAGAGAAAGGGGTAAAAAGAGAGACTGAAGCAGAAGTCCAAA
GAAATCCAAAGATAAAGAAAAATCTAAGTACAGA

Alignment

ORF - retro_cjac_2963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.77 %
• Parental protein coverage: 72.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRS
          IIKKINETFVDKDFVPY.DIRINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKG.S
Retrocopy IIKKINETFVDKDFVPY*DIRINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKG*S

Parental  AEEV-EEIKAEKEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIR
          AEEV.EEIKAEKEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIR
Retrocopy AEEV>EEIKAEKEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIR

Parental  DWKTGESLCYAFIEFEKEKHCEKAFFIMDNVLIIDDRRIHVDFSQSVAKVKWKGKEIGGKYTKSDFKEYE
          DWKTGESLCYAFIEFEKE..CEKAFF.MDNVLI.DDRRIHVDFSQSVAKVK.KGK..G.KYTKSDFKEYE
Retrocopy DWKTGESLCYAFIEFEKEEDCEKAFFKMDNVLI-DDRRIHVDFSQSVAKVKLKGK--GEKYTKSDFKEYE

Parental  KEQNNPSNLVLKDKVKPKQDAKYDLILDEQAEDSKSSHSHTSKKHKKKTRHCSEEKEDEDYMPIKNPNQD
          KEQNNPSNLVLKDKVKPKQDAKYDL.LDEQAEDSKSSH.HTSKKH.KKTRHCSEEKEDEDYMPIKNPNQD
Retrocopy KEQNNPSNLVLKDKVKPKQDAKYDLMLDEQAEDSKSSHAHTSKKHEKKTRHCSEEKEDEDYMPIKNPNQD

Parental  IYREMGFGHYEEEESCWEKQKSEKRDRTQNRSRSRSQERDGHYSNSHKSK-YQTDLYERERGKKRDRSRS
          IYREMGFGHYEEEESCWEKQKSEKRDRTQNRSRS.SQERDGH.SNSHKSK..QTDLYERERGKKRD.SRS
Retrocopy IYREMGFGHYEEEESCWEKQKSEKRDRTQNRSRS*SQERDGHHSNSHKSK<IQTDLYERERGKKRD*SRS

Parental  PKKSKDKEKSKYR
          PKKSKDKEKSKYR
Retrocopy PKKSKDKEKSKYR

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	1.13 RPM	11.05 RPM
SRP051959_heart	1.86 RPM	17.17 RPM
SRP051959_kidney	2.09 RPM	20.10 RPM
SRP051959_liver	1.19 RPM	11.20 RPM
SRP051959_lung	2.18 RPM	25.17 RPM
SRP051959_lymph_node	2.85 RPM	24.34 RPM
SRP051959_skeletal_muscle	1.24 RPM	12.10 RPM
SRP051959_spleen	2.10 RPM	23.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2963 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003145	5 retrocopies	retro_cjac_129, retro_cjac_1886, retro_cjac_2205, retro_cjac_3120, retro_cjac_4110,
Callithrix jacchus	ENSCJAG00000016094	1 retrocopy	retro_cjac_1302,
Callithrix jacchus	ENSCJAG00000019613	1 retrocopy	retro_cjac_2963 ,
Macaca mulatta	ENSMMUG00000023067	1 retrocopy	retro_mmul_1715,
Nomascus leucogenys	ENSNLEG00000015316	1 retrocopy	retro_nleu_173,
Oryctolagus cuniculus	ENSOCUG00000007696	2 retrocopies	retro_ocun_661, retro_ocun_892,
Taeniopygia guttata	ENSTGUG00000010655	1 retrocopy	retro_tgut_16,