RetrogeneDB ID: retro_cjac_12

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:12518710..12519526(-)
• Located in intron of: ENSCJAG00000011550

Retrocopy information

• Ensembl ID: ENSCJAG00000034991
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RFC2
• Ensembl ID: ENSCJAG00000003985
• Aliases: None
• Description: None

Sequence

>retro_cjac_12
ACCACAAGAATTCTATGCTTGGCACGAGCTCTGCTGGGCCCAGCACTCAAGGATGCTGTGTTGGAACTCAATGCTTCAAA
TGACAGGGGCATTGACGTTGTGAGGAATAAAATTAAAATGTTTGCTCAACAAAAAGTCACCCTTCCCAAAGGCCAACATA
AGATCATCATTCTGGATGAAGCCGACAGCATGACTGACGGAGCCCAGCAAGCCTTGAGGAGAACCATGGAAATCTACTCC
AAAACCACGTGCTTTGCCCTTGCTTGTAATGCTTCGGATAAGATCATTGAGCCCATTCAGTCCCGCTGCGCTGTCCTCCG
CTACACGAAGCTGACCGATGCCCAGATCCTCACCAGGCTGATGAGTGTTATCGAAAAGGAGAGGGTGCCCCACACTGATG
ACGGCCTGGAAGCCATCATCTTCATGGCGCAGGGAGACATGAGGCAGGCACTGAACAACCTGCAGTCCACCTTCTCAGGA
TTTGGCTTCATTAACAGTGAGAATGTTTTCAAGGTCTGTGATGAGCCCCACCCACTGCTGGTGAAGGAGATGATCCAGCA
CTGTGTGAACACCAGCATCGATGAAGCTTACAAGATTCTCGCTCACCTGTGGCATCTGGGCTACTCACCAGAAGATATCA
TTGGCAACATCTTTCGAGTGTCTAAAGCTTTCCAAATGGCAGAATACCTGAAACTGGAGTTTATCAAGGAAATTGGATAC
ACTCATATGAAAATCGCAGGAGTGAACTCCCTTTTGCAGATGGCAGGCCTCCTGGCCAGGCTGTGTCAGAAGACAATGGC
CCCGGTGGCCAGTTAG

Alignment

ORF - retro_cjac_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.96 %
• Parental protein coverage: 77.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTSILCLARALLGPALKDAVLELNASNDRGIDVVRNKVKMFAQHKVTLPKGRHKIIILDEADSMTDGAQQ
          TT.ILCLARALLGPALKDAVLELNASNDRGIDVVRNK.KMFAQ.KVTLPKG.HKIIILDEADSMTDGAQQ
Retrocopy TTRILCLARALLGPALKDAVLELNASNDRGIDVVRNKIKMFAQQKVTLPKGQHKIIILDEADSMTDGAQQ

Parental  ALRRTMEIYSKTTRFALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMSVIEKERVPHTDDGLEAII
          ALRRTMEIYSKTT.FALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMSVIEKERVPHTDDGLEAII
Retrocopy ALRRTMEIYSKTTCFALACNASDKIIEPIQSRCAVLRYTKLTDAQILTRLMSVIEKERVPHTDDGLEAII

Parental  FTAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNANIDEAYKILAHLWHLGYSP
          F.AQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVN..IDEAYKILAHLWHLGYSP
Retrocopy FMAQGDMRQALNNLQSTFSGFGFINSENVFKVCDEPHPLLVKEMIQHCVNTSIDEAYKILAHLWHLGYSP

Parental  EDIIGNIFRVCKTFQMAEYLKLEFIKEIGYTHMKIAEGVNSLLQMAGLLARLCQKTMAPVAS
          EDIIGNIFRV.K.FQMAEYLKLEFIKEIGYTHMKIA.GVNSLLQMAGLLARLCQKTMAPVAS
Retrocopy EDIIGNIFRVSKAFQMAEYLKLEFIKEIGYTHMKIA-GVNSLLQMAGLLARLCQKTMAPVAS

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	8.54 RPM
SRP051959_heart	2.28 RPM	6.45 RPM
SRP051959_kidney	0.31 RPM	5.64 RPM
SRP051959_liver	0.02 RPM	7.39 RPM
SRP051959_lung	0.07 RPM	8.43 RPM
SRP051959_lymph_node	0.02 RPM	10.55 RPM
SRP051959_skeletal_muscle	0.07 RPM	4.89 RPM
SRP051959_spleen	0.02 RPM	7.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_12 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_12 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003985	1 retrocopy	retro_cjac_12 ,
Otolemur garnettii	ENSOGAG00000014927	1 retrocopy	retro_ogar_941,