RetrogeneDB ID: retro_cjac_1874

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:186955880..186956149(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002551
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPPDE2
• Ensembl ID: ENSCJAG00000018941
• Aliases: None
• Description: None

Sequence

>retro_cjac_1874
TTCTTCGGCAGTGGTGGTATCTCCAGCTGCCCTCCGGGAGGGACATTGCTTGGGCCCCCAGACTCTGTGGTTGATGTGGG
GAGTACAGAAGTCACAGAAGAAATCTTTCTGGAGTACCTGTCCTCCCTGGGGGAGTCCCTGTTCCGAGGTGAGGCCTACA
ACCTCTTTGAACACAACTGTAACACCTTCAGCAAGAAGTGGCACAGTTCCTGACTGGGCTGAAGATTCCTTGTTACATCA
CAGACCTGCCCTCTGAAGCTCGCTCCACG

Alignment

ORF - retro_cjac_1874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.81 %
• Parental protein coverage: 66.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FFGSGGISSCPPGGTLHGPPDSVVDVGSTEVTEEIFLEYPSSLGESLFRAEAYNLFKHNGNTFS-NEVAQ
          FFGSGGISSCPPGGTL.GPPDSVVDVGSTEVTEEIFLEY.SSLGESLFR.EAYNLF.HN.NTFS..EVAQ
Retrocopy FFGSGGISSCPPGGTLLGPPDSVVDVGSTEVTEEIFLEYLSSLGESLFRGEAYNLFEHNCNTFS<QEVAQ

Parental  FLSGRKIPSYITDLPSEVLST
          FL.G.KIP.YITDLPSE..ST
Retrocopy FLTGLKIPCYITDLPSEARST

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	0.58 RPM	0.67 RPM
SRP051959_heart	0.39 RPM	0.56 RPM
SRP051959_kidney	0.75 RPM	0.93 RPM
SRP051959_liver	1.08 RPM	1.58 RPM
SRP051959_lung	0.34 RPM	0.86 RPM
SRP051959_lymph_node	0.27 RPM	0.68 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.50 RPM
SRP051959_spleen	0.32 RPM	0.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1874 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1874 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018941	1 retrocopy	retro_cjac_1874 ,
Echinops telfairi	ENSETEG00000005136	1 retrocopy	retro_etel_2107,
Monodelphis domestica	ENSMODG00000016577	2 retrocopies	retro_mdom_1548, retro_mdom_684,
Ictidomys tridecemlineatus	ENSSTOG00000009480	1 retrocopy	retro_itri_1719,