RetrogeneDB ID: retro_cjac_3883

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285785.1:47923..49005(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009971
• Aliases: None
• Description: None

Sequence

>retro_cjac_3883
ATGCCGCGGGTGTATATCGGCCGCCTGAGCTACCAGACCCGGGAGCGCGATGTGGAGTGCTTCTTTAAAGGCTACGGGAA
GATCCTGGAGGTGGATCTGAAGAACGGATATGGTTTTGTGGAGTTCGATGATCTGCGTGATGCAGATGATGCTGTTTATG
AACTGAATGGCAAAGACCTTTGTGGTGAGCGAGCGGTTGTTGAGCATGCCCGCGGCCCACGGCGAGATGGCAGTTACGGT
TCTGGACGCAGTGGATATGGTTAAAGAAGAAGTGGCCGAGATAAATATGGCCCTCCTACTCGCACAGAGTACAGGCTTAT
TGTGGGGAATTTGTCAAGTCGGTGCAGCTGGCAAGACCTAAAGGATTATATGCGTCAGGCAGGAGAAGTGACTTATGCAG
ACGCTCACAAGGGACGCAAAAGTGAAGGAGTGATTGAATTTGGATCTTATTCTGATATGAAAAGAGCTTTGGAAAAGTTG
GATGGAACTGAAGTCAATGGCAGAAAAATCCGATTAGTTGAAGACAAGCCAGGTTCTAGATGACGCGGGTCCTATTCCAG
GAGCCGGAGCCATTCAAGGTCTCGCTCTCGAAGCAGACATTCCCGTAAGAGCAGAAGCCGAAATGGAAGCAGCAAAATCA
GTCATTCCAAGAGTAGATCCCGGTCCAGGTCGGGCCCCACTCCCAGAGCAAGAGCCGGAGCCGAAGCCAGAGTCGGCGCC
GGAGCCAGAAGGAGAAAAGCAGGAGCCGCAGCAAGGACAAGAGCCGCAGCCGCAGTCGCAGCGAAGGCAAGAGCCGAAGC
AAAAGCAAAGACCAAGCAGAAGAGAAGATCCAAAACAATGACAATGCTGGGAAACCTAAGAGCTGGAGTCCTAGCAGGCA
TAAAAGTAAGAGCAGGAGTCAGGAGGAGGAGAAGCGAGGGAGTATGAGCAGGGGCAGGAGCCAGGAGGCGGGCAGGGGCC
AGGAGAATAGCCTCTGCCAGAGTCGGAGCCGGAGCAGGAGCAAAGTGGGTAGCAGGAGCCGGAGGAGGAGCCACAGCAAG
AGCAAGGACAAGAGGAAGGGCAGGAAGAGAAGCAGGGAGGAG

Alignment

ORF - retro_cjac_3883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.47 %
• Parental protein coverage: 73.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPRVYIGRLSYQARERDVERFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHA
          MPRVYIGRLSYQ.RERDVE.FFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGER..VEHA
Retrocopy MPRVYIGRLSYQTRERDVECFFKGYGKILEVDLKNGYGFVEFDDLRDADDAVYELNGKDLCGERAVVEHA

Parental  RGPRRDGSYGSGRSGYGYRRSGRDKYGPPTRTEYRLIVENLSSRCSWQDLKDYMRQAGEVTYADAHKGRK
          RGPRRDGSYGSGRSGYG.RRSGRDKYGPPTRTEYRLIV.NLSSRCSWQDLKDYMRQAGEVTYADAHKGRK
Retrocopy RGPRRDGSYGSGRSGYG*RRSGRDKYGPPTRTEYRLIVGNLSSRCSWQDLKDYMRQAGEVTYADAHKGRK

Parental  NEGVIEFVSYSDMKRALEKLDGTEVNGRKIRLVEDKPGSRRRRSYSRSRSHSRSRSRSRHSRKSRSRSGS
          .EGVIEF.SYSDMKRALEKLDGTEVNGRKIRLVEDKPGSR.R.SYSRSRSHSRSRSRSRHSRKSRSR.GS
Retrocopy SEGVIEFGSYSDMKRALEKLDGTEVNGRKIRLVEDKPGSR*RGSYSRSRSHSRSRSRSRHSRKSRSRNGS

Parental  SKSSHSKSRSRSRS-GSHSRSKSRSRSQSRSRSKKEKSRSPSKDKSRSRSRSIGKSRSKSKDQAEEKIQN
          SK.SHSKSRSRSRS.G.HS................EKSRS.SKDKSRSRSRS.GKSRSKSKDQAEEKIQN
Retrocopy SKISHSKSRSRSRS<GPHSXXXXXXXXXXXXXXXXEKSRSRSKDKSRSRSRSEGKSRSKSKDQAEEKIQN

Parental  NDNAGKPKSRSPSRHKSKSKSRSRSQERRVEEEKRGSMSRGRARRQQEKSLRQSRSRSRSKGGSRSRSRS
          NDNAGKPKS.SPSRH..KSKSRS...E.R.......S...GR....QE.SL.QSRSRSRSK.GSRSR.RS
Retrocopy NDNAGKPKSWSPSRH--KSKSRSQEEEKRGSMSRGRSQEAGRG---QENSLCQSRSRSRSKVGSRSRRRS

Parental  HSKSKDKRKGRKRSREE
          HSKSKDKRKGRKRSREE
Retrocopy HSKSKDKRKGRKRSREE

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	0.02 RPM	11.94 RPM
SRP051959_heart	0.19 RPM	16.03 RPM
SRP051959_kidney	0.02 RPM	11.78 RPM
SRP051959_liver	0.00 RPM	13.02 RPM
SRP051959_lung	0.03 RPM	23.51 RPM
SRP051959_lymph_node	0.00 RPM	19.36 RPM
SRP051959_skeletal_muscle	0.07 RPM	10.70 RPM
SRP051959_spleen	0.02 RPM	16.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3883 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013858	1 retrocopy	retro_chof_1058,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Callithrix jacchus	ENSCJAG00000009971	3 retrocopies	retro_cjac_3688, retro_cjac_3883 , retro_cjac_3899,
Callithrix jacchus	ENSCJAG00000016062	5 retrocopies	retro_cjac_1035, retro_cjac_1969, retro_cjac_2006, retro_cjac_620, retro_cjac_746,
Microcebus murinus	ENSMICG00000008965	1 retrocopy	retro_mmur_1597,
Otolemur garnettii	ENSOGAG00000015515	1 retrocopy	retro_ogar_2205,