RetrogeneDB ID: retro_cjac_153

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:24906475..24907678(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023028
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014995
• Aliases: None
• Description: None

Sequence

>retro_cjac_153
ATGATGGGCTTGGGAAACGGGCGTCGCAGCATGAAGTCGCCGCCCCTCGTGCTGGCTGCCCTGGTGGCCTGCGTCATCTT
CTTGGGCTTCAACTACTGGATTGCTAGCTCCCGGAGCGTGGATCTCCAGACGCGGATCATGGAGCTGGAAGGCAGGGTCG
GCAGGGCAGCCGCAGAGAGAGGTGCCGTGGAACTGAAGAAGAACGAGTTCCAGGGAGAGCTGGAGAAGCAGCGGGAGCAG
CTTGACAAAATCCAGTCCAGCCACAACTTCCAGCTGGAGAGTGTCAACAAGCTGTACCAGGACGAAAAGGCGGTTTTGGT
GAATAACATCATCACAGGTGAGAGGCTCATCCGAGTGCTGCAAGACCAGCTAAAGACCCTGCAGAGGAATTACGGCAGGC
TGCAGCAGGATGTCCTCCAGTTTCAGAAGAACCAGACCAACCTAGAGAGGAAGTTCTCCTACGACCTGAGCCAATGCATC
AATCAGATGAAGGAACAGTGTGAGGAGCGAATAGAAGAGGTCACCAAAAAGGGGAACGAAGCTGTAGCTTCCAGAGACCT
GAGTGAAAACAACGACCAGAGTCAGCAGCTCCAAGACCTCAGCAAGCCTCAGCCCAGGCTGCAGGCGGCAGGCCTGCCAC
GCACAGAGGTGCCACAAGGGAAAGGAAAGATGCCCAGCAACAGCAAGTCCCAGACACCAGCCCCCAGGTCCGAAGTGGCT
GTGGATTCCAAGAGACAAGCTGAGAAAGAGGAAGCCAATGAGATCCAGGTGGTGAGTGAGGAAGAGCCTCAGAGGGACAG
GCTGCAGCTGCCGCAGGAACCAGGCCGGGAGCAGGTGGCAGAAGACAGACCTGTGGGCAGAAGAGGCTTCGGGGGAACTA
GAGAACTGGGCCAGACTCCACAGGTGGCAGCTGCCCTGTCGGTGAGCCAGGAAAATCAGGAGGCTGAGGGCCCTGAGCGA
GACCAGCTTGTCATCCCCGATGGACAGGAGGAGGAGCAGGAAGCTGCCGAGGAAGGGAGAAACCAGCAAAAACTGAGAGC
TGAAGATGACTACAACATGGATGAAAATGAGGCGGAATCTGAAACAGACAAGCAGGCAGCCCTGGCAGGGAATGACAGAA
ACATAGATGTTTTTAATGAAGATCAGAAAAGAGACATCATAAATTTACTTGATCAGCATGAAAAGCGAAATCATACGCTC
TGA

Alignment

ORF - retro_cjac_153 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.34 %
• Parental protein coverage: 98.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAVLVNNITTGERLIRVLQDQLKTLQRNYGRLQQDVLQFQKNQTNLERKFSYDLSQCINQMKEVKEQCEE
          .AVLVNNI.TGERLIRVLQDQLKTLQRNYGRLQQDVLQFQKNQTNLERKFSYDLSQCINQM...KEQCEE
Retrocopy KAVLVNNIITGERLIRVLQDQLKTLQRNYGRLQQDVLQFQKNQTNLERKFSYDLSQCINQM---KEQCEE

Parental  RIEEVTKKGNEAVASRDLSENNDQSQQLHDLSKPQPRLQAAGLPRTEVPQGKGKMPSNSKSQTPAPSSEV
          RIEEVTKKGNEAVASRDLSENNDQSQQL.DLSKPQPRLQAAGLPRTEVPQGKGKMPSNSKSQTPAP.SEV
Retrocopy RIEEVTKKGNEAVASRDLSENNDQSQQLQDLSKPQPRLQAAGLPRTEVPQGKGKMPSNSKSQTPAPRSEV

Parental  AVDSKRQAEKEEANEIQVVSEEEPQRDRLQLPQEPGREQVAEDRPVGRRGFGGTRELGQTPQVAAALSVS
          AVDSKRQAEKEEANEIQVVSEEEPQRDRLQLPQEPGREQVAEDRPVGRRGFGGTRELGQTPQVAAALSVS
Retrocopy AVDSKRQAEKEEANEIQVVSEEEPQRDRLQLPQEPGREQVAEDRPVGRRGFGGTRELGQTPQVAAALSVS

Parental  QENQEAEGPERDQLVIPDGQEEEQEAAEEGRNQQKLRAEDDYNMDENEAESETDKQAALAGNDRNIDVFN
          QENQEAEGPERDQLVIPDGQEEEQEAAEEGRNQQKLRAEDDYNMDENEAESETDKQAALAGNDRNIDVFN
Retrocopy QENQEAEGPERDQLVIPDGQEEEQEAAEEGRNQQKLRAEDDYNMDENEAESETDKQAALAGNDRNIDVFN

Parental  EDQKRDTINLLDQHEKRNHTL
          EDQKRD.INLLDQHEKRNHTL
Retrocopy EDQKRDIINLLDQHEKRNHTL

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	10.03 RPM	63.97 RPM
SRP051959_heart	1.16 RPM	6.17 RPM
SRP051959_kidney	1.38 RPM	9.47 RPM
SRP051959_liver	0.09 RPM	1.43 RPM
SRP051959_lung	1.59 RPM	12.36 RPM
SRP051959_lymph_node	0.39 RPM	2.19 RPM
SRP051959_skeletal_muscle	0.48 RPM	2.56 RPM
SRP051959_spleen	1.09 RPM	6.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_153 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_153 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	ENSCJAG00000014995	1 retrocopy	retro_cjac_153 ,
Microcebus murinus	ENSMICG00000017724	1 retrocopy	retro_mmur_22,