RetrogeneDB ID: retro_cjac_3556

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01184401.1:4329..5036(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HOMER2
• Ensembl ID: ENSCJAG00000015884
• Aliases: None
• Description: None

Sequence

>retro_cjac_3556
GAACAGCCCATTCTCACCCGAGCCCACGGCTTCCAGATCGACCCCAACATCAGGAAGAACCGGATCCTGCGAGCTCAGCG
GTCACCGTTTCCTCCTTCTATGACGTCACAGGAACCGCTGTCAGATCGTCAGCGTGGGCGGGGCCAAGGCGACCATCAAC
AGCACAATCGCAACAAATACGCCCTTCCCCAAAACGCCACAGAAGTCTGGGCAGGGCCGACAGCGGAGCCCACACGGTGT
TTGGTTTGGGGTTTTCCTCTGAGCAGCAGCTGACAACGTTTGCAGAGAAATTCCAGGAGCTGGAGGAAGCTGCCGAGATG
CCCAAAGACAAGGCCCGGGAGAAAACCGAGACCTGGAGTCACGGTTCCCAGTGATCTGGGCGTGAAGCCCCATCTGCGGC
TGCGGCATCCAGTGTCGAGGGCGGCGGTGAAAAGGCCTCTCAGCCGCTGCAGCCGACACGCACCGGAAGTCTGGGAAGGA
CGCGCTGAGATTGCCCTGACGCAGAGCGCGGCCACCGCGCAGGAGTGGAAGCTGCAGCCGCAGCCCCTGAGGAGAGCCAC
GCCCCGCGGACCACAGCGCTGCAGGAGGCGGCGGCCAGCGCGGAGCCGGGAAGAGGCCGGGACACCAACAGGGAGGAGCA
GAAGAACACGCTGCTCAAGAGGAGGATGGAGGAGCTGGAGGCGGAGCTCCGAGAACAGGAGACAGAG

Alignment

ORF - retro_cjac_3556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.09 %
• Parental protein coverage: 67.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EQPIFTTRAHVFQIDPNTKKNWM-PASKQAVTVSYFYDVT-RNSYRIISVDGAKVIINSTITPNMTFT-K
          EQPI.T.RAH.FQIDPN..KN...PAS..AVTVS.FYDVT.RN...I.SV.GAK..INSTI..N..F..K
Retrocopy EQPILT-RAHGFQIDPNIRKNRI<PASS-AVTVSSFYDVT<RNRCQIVSVGGAKATINSTIATNTPFP>K

Parental  TSQKFGQWADSRANTVFGLGFSSEQQLTKFAEKFQEVKEAAKIAKDKTQEKIETSSNHSQESGRETPSST
          .....G..ADS.A.TVFGLGFSSEQQLT.FAEKFQE..EAA...KDK..EK.ET.S..SQ.SGRE.PS..
Retrocopy RHRSLGR-ADSGAHTVFGLGFSSEQQLTTFAEKFQELEEAAEMPKDKAREKTETWSHGSQ*SGREAPSAA

Parental  QASSVNGTDDEKASH-AGPADTHLKSENDKLK-IALTQSAANVKKWEIELQTLR-ESNARLTTALQESAA
          .ASSV.G...EKAS..A..ADTH.KS..D.L..IALTQSAA....W....Q.LR.ES.A..TTALQE.AA
Retrocopy AASSVEG-GGEKASQ<AAAADTHRKSGKDALR<IALTQSAATAQEWKLQPQPLR<ESHAPRTTALQEAAA

Parental  SVEQWK-RQFSICRDENDQLRNKIDELEEQCSEINRE
          S.E....R........N..L.....ELE....E...E
Retrocopy SAEPGRGRDTNREEQKNTLLKRRMEELEAELREQETE

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	1.89 RPM
SRP051959_heart	0.00 RPM	6.65 RPM
SRP051959_kidney	0.00 RPM	10.18 RPM
SRP051959_liver	0.00 RPM	33.34 RPM
SRP051959_lung	0.00 RPM	8.04 RPM
SRP051959_lymph_node	0.00 RPM	1.92 RPM
SRP051959_skeletal_muscle	0.00 RPM	26.36 RPM
SRP051959_spleen	0.00 RPM	1.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3556 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3556 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3556 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015884	3 retrocopies	retro_cjac_3556 , retro_cjac_3614, retro_cjac_3871,
Cavia porcellus	ENSCPOG00000014688	1 retrocopy	retro_cpor_35,
Equus caballus	ENSECAG00000023619	3 retrocopies	retro_ecab_1046, retro_ecab_661, retro_ecab_692,
Homo sapiens	ENSG00000103942	1 retrocopy	retro_hsap_1468,
Macaca mulatta	ENSMMUG00000008297	1 retrocopy	retro_mmul_2278,
Nomascus leucogenys	ENSNLEG00000010953	1 retrocopy	retro_nleu_3002,
Pongo abelii	ENSPPYG00000006735	5 retrocopies	retro_pabe_1209, retro_pabe_1210, retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,