RetrogeneDB ID: retro_cjac_3222

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:60189096..60189593(+)
• Located in intron of: ENSCJAG00000001472

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018863
• Aliases: None
• Description: None

Sequence

>retro_cjac_3222
GAGGTGGTCCTCACAATGGAGAGCCAGGAAATAGAATGGGAAGTGGGAGATGCAATGGTCATTGGAAAGAAAGACAGGAC
ATCAAGGCCACAGATGCCATAGCCCATGCAGCTGGCTTCACTGTGTCTCACGACGTGACTGCTCCTGATCTTGCAAATGA
GATGTAAGGGGAAACACTGGCTGCTGGGAAAAATCTCTGGCACCTTTTGCCCTCTGGGCCCTATCTTGGTGACCAAGGAC
AGTGTAGCAGAACCACACAACTTAAAGATCTGCTGCTGAGTGAAAGAGAATGTGATCCAGAACACCCACCAGATGGTGTT
CAAGACGGAAGAGCCAATAACCTGGGTCTCCCAGTTTGTCACCTTCTATCCAGGGGATGTCATCCTGACTGGGACCTCCC
CAGGTATCAGTGAATTTAGGAAACTTCCTGTCCTAAGAAGAGGGATGAAGTCCAGTGTGAGATTGAAGAGCTAGGTGTCA
TCATCAACAAGGTGGTG

Alignment

ORF - retro_cjac_3222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.84 %
• Parental protein coverage: 53.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVVLPPESQEVDWEVELAVVIGKKGK-HIKATDAMAHVAGFTVAHDVSARDW-QMRRNGKQWLLGKTFDT
          EVVL..ESQE..WEV..A.VIGKK....IKATDA.AH.AGFTV.HDV.A.D..QMR..GK.WLLGK...T
Retrocopy EVVLTMESQEIEWEVGDAMVIGKKDR<DIKATDAIAHAAGFTVSHDVTAPDL>QMRCKGKHWLLGKISGT

Parental  FCPLGPALVTKDSVADPHNLKICCRVNGEVVQSSNTKQMVFKTEELIAWVSQFVTFYPGDVILTGTPPGV
          FCPLGP.LVTKDSVA.PHNLKICC.V...V.Q..NT.QMVFKTEE.I.WVSQFVTFYPGDVILTGT.PG.
Retrocopy FCPLGPILVTKDSVAEPHNLKICC*VKENVIQ--NTHQMVFKTEEPITWVSQFVTFYPGDVILTGTSPGI

Parental  GVFRKPPVFLKKG-DEVQCEIEELGVIINKVV
          ..FRK.PV.L..G.DEVQCEIEELGVIINKVV
Retrocopy SEFRKLPV-LRRG<DEVQCEIEELGVIINKVV

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	4.68 RPM
SRP051959_heart	0.02 RPM	8.91 RPM
SRP051959_kidney	0.02 RPM	16.82 RPM
SRP051959_liver	0.11 RPM	15.47 RPM
SRP051959_lung	0.65 RPM	6.20 RPM
SRP051959_lymph_node	0.00 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.31 RPM
SRP051959_spleen	0.29 RPM	6.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3222 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3222 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018863	1 retrocopy	retro_cjac_3222 ,
Homo sapiens	ENSG00000144199	1 retrocopy	retro_hsap_1025,
Gorilla gorilla	ENSGGOG00000016246	1 retrocopy	retro_ggor_810,
Macaca mulatta	ENSMMUG00000012859	1 retrocopy	retro_mmul_818,
Nomascus leucogenys	ENSNLEG00000000008	1 retrocopy	retro_nleu_903,
Pongo abelii	ENSPPYG00000012057	1 retrocopy	retro_pabe_860,
Pan troglodytes	ENSPTRG00000012214	1 retrocopy	retro_ptro_700,