RetrogeneDB ID: retro_cjac_3452

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01180228.1:2231..2994(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000036005
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009532
• Aliases: None
• Description: None

Sequence

>retro_cjac_3452
ATGAGCTAGCTGCCCGCCGACGTGCGGGCCTTCCTGCGGGAGCACAGAGCCTGCAGCTGCAGCCGGACGCCCGCAAGGCC
AGGTGCATCCTGACAGGTCAGGAGCTGCCCTGCCGCCTGCCGGAGTTCCAGGTCTACACCCACGGCAGGAAGTACCAACG
GCTGGTCCGCGCCTCCCCGGCTTTCAACTATGCAGAGTTTGAACCGCACAGCGTGCCCAGCACCAAGAACCCGCGCCAGT
TGTTCTGCAAACTCACCCTGCGGCACATCAACAAGTGCCCAGAACACGTGCTGAGGCACATCCAGGGCCGGCAGTACCAG
CGAGCTCTGTGTAAATATGCAGAATGTCAGAAGCAAGGGCTGGAGTACATTACTGCGTGCCTGGTGCACCGGAGGAGAAA
GAGGGAGGACCGGATGGACGGTGATGGGCCTCGCTTGTGGGAAGCCTTCTGGGAGCCCATGTCCAGTGATGAGGGGGGAG
CTCCAAGTGACGACAGCATGACAGACCTGTACCCACCCGAGCTATTTACCAGAAAGGACCTTTGAAACACAGAGGACATG
GATGGCACTGATGACTTTTTGACAAACGAAGAGGACAAGGAGGCAAAGCCCCCAGAGCGTCCACTGATGAAGGCAGGAAG
GAGACGGACATGGACTGGGGGCTGGTCTGGAAGCGCAGGAAGAAGCAGTTGGGCTCCTTGAAAAAGAAGTTCAAGAGTCA
TCCCCGCAAACCTAAGAGCTTCAGCTCCTGTAAACAGCCAGGT

Alignment

ORF - retro_cjac_3452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSELPADVRAFLREH-PSLRLQPDSRKVRCILTGHELPCRLPELQVYTRGKKYQRLVRASPAFDYAEFEP
          MS.LPADVRAFLREH..SL.LQPD.RK.RCILTG.ELPCRLPE.QVYT.G.KYQRLVRASPAF.YAEFEP
Retrocopy MS*LPADVRAFLREH<QSLQLQPDARKARCILTGQELPCRLPEFQVYTHGRKYQRLVRASPAFNYAEFEP

Parental  HIVPSTKNPXQLFCKLTLRHINKCPEHVLRHIQGRRYQRALDKYAECQKQGLEYVPACLVH-RRKREDQM
          H.VPSTKNP.QLFCKLTLRHINKCPEHVLRHIQGR.YQRAL.KYAECQKQGLEY..ACLVH.RRKRED.M
Retrocopy HSVPSTKNPRQLFCKLTLRHINKCPEHVLRHIQGRQYQRALCKYAECQKQGLEYITACLVHRRRKREDRM

Parental  DGDGPRSWEAFWEPMSSDEGGAPSDDSMTDLYPPELFTRKDLGNTEDMDGTDDFLTDEEDEETKP-LRQS
          DGDGPR.WEAFWEPMSSDEGGAPSDDSMTDLYPPELFTRKDL.NTEDMDGTDDFLT.EED.E.KP..R.S
Retrocopy DGDGPRLWEAFWEPMSSDEGGAPSDDSMTDLYPPELFTRKDL*NTEDMDGTDDFLTNEEDKEAKP<PRAS

Parental  T--GRRETDVDWGLVRKRRKKQLGSLKKKFKSHPRKPKSFSSCKQPG
          T..GR.ETD.DWGLV.KRRKKQLGSLKKKFKSHPRKPKSFSSCKQPG
Retrocopy TDEGRKETDMDWGLVWKRRKKQLGSLKKKFKSHPRKPKSFSSCKQPG

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	0.00 RPM	1.82 RPM
SRP051959_heart	0.00 RPM	1.89 RPM
SRP051959_kidney	0.00 RPM	2.29 RPM
SRP051959_liver	0.00 RPM	3.40 RPM
SRP051959_lung	0.00 RPM	1.90 RPM
SRP051959_lymph_node	0.00 RPM	3.01 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.91 RPM
SRP051959_spleen	0.00 RPM	1.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3452 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019763	1 retrocopy	retro_cfam_1702,
Callithrix jacchus	ENSCJAG00000009532	5 retrocopies	retro_cjac_3362, retro_cjac_3452 , retro_cjac_3606, retro_cjac_3648, retro_cjac_3914,
Felis catus	ENSFCAG00000028927	1 retrocopy	retro_fcat_277,
Monodelphis domestica	ENSMODG00000012766	1 retrocopy	retro_mdom_1894,