RetrogeneDB ID: retro_cjac_1088

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38635501..38636129(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006523
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015686
• Aliases: None
• Description: None

Sequence

>retro_cjac_1088
ATGCGCTGCTTGACCACGCCCATGCTGCTGCGAGCCCTGGCCCAGGCTGCCGGTGCAGGACCTCCCGGTCACTGGAGCCT
CCACAGCAGTGCAGTGGCAGCCACCTACAAGCATGTGAACATGCAGGAGCCCAAGATGGACATGAGGTCAATGACTGACC
GGGAAGCCCAGACCCTGCTGTGGACTGAGCTCCCCCGAGGCCTGGCCATGACCCTGAGCTACCCGTTCTGGGAGCCGGCT
ACCATCAACTATCCATTCGAGAGGGGCCCACTGAGCCCTCGCTTCCGTGGGGAGCATGCCCTGCGCCGGTACCCATCTGG
GGAGGAGCGCTGCATTGCCTGCAAGCTCTGTGAGGCCATCTGCCCCGCCCAGGCCATCATATCGAGGCTGAGCCGAGAGC
TGATGGCAGCCGCCGGACCACTCGCTATGACATCGACATGACCAAGTACATCTATTGTGGCTTCTGCCAGGAGGCCTGCC
CCGTGGACGCCATAGTCAAGGGCCCCAACTTTGAGTTCTCCAAGAGACGCATGAGGAGCTGCTGTACAACAAGGAGAAGC
TGCTCAACAACCGGGACAAGTGGGAGGCTGAGATCGCTGCCAATATCCAGGCTGACTACCTGTACCGT

Alignment

ORF - retro_cjac_1088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRCLTTPMLLRALAQAARAGPPGSRSLHSSAVAATYKHVNMQEPKMDMRSVTDRAAQTLLWTELFRGLAM
          MRCLTTPMLLRALAQAA.AGPPG..SLHSSAVAATYKHVNMQEPKMDMRS.TDR.AQTLLWTEL.RGLAM
Retrocopy MRCLTTPMLLRALAQAAGAGPPGHWSLHSSAVAATYKHVNMQEPKMDMRSMTDREAQTLLWTELPRGLAM

Parental  TLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAIT-IEAEPRADGSRR
          TLSY.F.EPATINYPFE.GPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAI..IEAEPRADGSRR
Retrocopy TLSYPFWEPATINYPFERGPLSPRFRGEHALRRYPSGEERCIACKLCEAICPAQAII<IEAEPRADGSRR

Parental  TTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFS-TETHEELLYNKEKLLNNGDKWEAEIAANIQADYL
          TTRYDIDMTK.IYCGFCQEACPVDAIV.GPNFEFS..ETHEELLYNKEKLLNN.DKWEAEIAANIQADYL
Retrocopy TTRYDIDMTKYIYCGFCQEACPVDAIVKGPNFEFS<QETHEELLYNKEKLLNNRDKWEAEIAANIQADYL

Parental  YR
          YR
Retrocopy YR

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	0.09 RPM	7.23 RPM
SRP051959_heart	0.02 RPM	20.94 RPM
SRP051959_kidney	0.02 RPM	12.54 RPM
SRP051959_liver	0.09 RPM	12.63 RPM
SRP051959_lung	0.00 RPM	5.32 RPM
SRP051959_lymph_node	0.00 RPM	6.89 RPM
SRP051959_skeletal_muscle	0.28 RPM	35.57 RPM
SRP051959_spleen	0.02 RPM	4.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1088 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1088 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1088 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001217	2 retrocopies	retro_amel_366, retro_amel_613,
Canis familiaris	ENSCAFG00000011083	2 retrocopies	retro_cfam_1258, retro_cfam_129,
Callithrix jacchus	ENSCJAG00000015686	4 retrocopies	retro_cjac_1088 , retro_cjac_1652, retro_cjac_2237, retro_cjac_3810,
Macropus eugenii	ENSMEUG00000015013	2 retrocopies	retro_meug_1148, retro_meug_926,
Myotis lucifugus	ENSMLUG00000017611	1 retrocopy	retro_mluc_1771,
Mustela putorius furo	ENSMPUG00000004193	1 retrocopy	retro_mputfur_592,
Otolemur garnettii	ENSOGAG00000013220	1 retrocopy	retro_ogar_2669,
Xenopus tropicalis	ENSXETG00000020882	1 retrocopy	retro_xtro_50,