RetrogeneDB ID: retro_cjac_3648

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01192270.1:1936..2698(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000037331
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3648
ATGAGCTAGCTGCCCGACGACGTGCGGGCCTTCCTGCGCGAGCACAGAGCCTGCGGCTGCAGCCGGACGCCCGCAAGGCC
AGGTGCATCCTGACAGGTCAGGAGCTGCCCTGACGCCTGCCGGAGTTCCAGGTCTACAACCGCGGCAGGAAGTACCAGCG
GCTGGTGCGCGCCTCCTCTGCTTTCAACTATGCAGAGTTTGAACCGCACATCATGCCCAGCACCAAGAACCCGCGCCAGT
TGTTCTGCAAACTCACCCTGCGGCACATCAACAAGTGCCCAGAACACGTGCTGAGGCACATCCAGGGCCGGCAGTACCAG
CGAGCTCTGTGTAAATATGCAGAATGTCAGAAGCAAGGGCTGGAGTACATTACTGCGTGCCTGGTGCACCGGAGGAGAAA
GAGGGAGGACCGGATGGACGGTGATGGGCCTCGCTTGTGGGAAGCCTTCTGGGAGCCCATGTCCAGTGATGAGGGGGGAG
CTCCAAGTGACGACAGCATGACAGACCTGTACCCACCCGAGCTATTTACCAGAAAGGACCTTTGAAACACAGAGGACATG
GATGGCACTGATGACTTTTTGACAAACGAAGAGGACAAGGAGGCAAAGCCCCAGAGCGTCCACTGATGAAGGCAGGAAGG
AGACGGACATGGACTGGGTGCTGGTCTGGAAGCGCAGGAAGAAGCAGTTGGGCTCCTTGAAAAAGAAGTTCAAGAGTCAT
CCCCGCAAACCTAAGAGCTTCAGCTCCTGTAAACAGCCAGGT

Alignment

ORF - retro_cjac_3648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSELPADVRAFLREH-PSLRLQPDSRKVRCILTGHELPCRLPELQVYTRGKKYQRLVRASPAFDYAEFEP
          MS.LP.DVRAFLREH..SLRLQPD.RK.RCILTG.ELP.RLPE.QVY.RG.KYQRLVRAS.AF.YAEFEP
Retrocopy MS*LPDDVRAFLREH<QSLRLQPDARKARCILTGQELP*RLPEFQVYNRGRKYQRLVRASSAFNYAEFEP

Parental  HIVPSTKNPXQLFCKLTLRHINKCPEHVLRHIQGRRYQRALDKYAECQKQGLEYVPACLVH-RRKREDQM
          HI.PSTKNP.QLFCKLTLRHINKCPEHVLRHIQGR.YQRAL.KYAECQKQGLEY..ACLVH.RRKRED.M
Retrocopy HIMPSTKNPRQLFCKLTLRHINKCPEHVLRHIQGRQYQRALCKYAECQKQGLEYITACLVHRRRKREDRM

Parental  DGDGPRSWEAFWEPMSSDEGGAPSDDSMTDLYPPELFTRKDLGNTEDMDGTDDFLTDEEDEETKPLRQST
          DGDGPR.WEAFWEPMSSDEGGAPSDDSMTDLYPPELFTRKDL.NTEDMDGTDDFLT.EED.E.KP.....
Retrocopy DGDGPRLWEAFWEPMSSDEGGAPSDDSMTDLYPPELFTRKDL*NTEDMDGTDDFLTNEEDKEAKPQSVH*

Parental  GRRETD-VDWGLVRKRRKKQLGSLKK-KFKSHPRKPKSFSSCKQPG
          .R.E.D....G..........G.L.K.KFKSHPRKPKSFSSCKQPG
Retrocopy *RQEGDGHGLGAGLEAQEEAVGLLEK>KFKSHPRKPKSFSSCKQPG

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_3648 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3648 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,