RetrogeneDB ID: retro_cjac_3743

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01198121.1:1258..1729(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL9
• Ensembl ID: ENSCJAG00000012890
• Aliases: None
• Description: myosin, light chain 9, regulatory [Source:HGNC Symbol;Acc:15754]

Sequence

>retro_cjac_3743
CAGAGCAGCCCATCCAATGTCTTCGCGATGTTTGACCAGTTCCACATCCAGGAGTTCAAGGAGGCTTTCAACATGATTGA
CCAGAACTGTGAAGGCTTCGTTCACAAGGGGGACCTGAAGGACAAGCTGGCCTGACTGGGGAAGAACCCCAAGAATGAAT
ACCTGGAGAGTATAATAAGCAAGGCCCCGAGGCCCATCAACTTAACCACTTTCCTCACCATGTTTGGGAAGAAGCTGAAC
GGCAGGGACCCCAAGGATGTGATCCAAAATGCCTTTGCCTGCTTCAATTAGGAAGCCTCAGGTTTCTTCCATGAGGACCA
CCTCTGGGAGCTGCTCACCACCATGGGTGACAGCTTCACAGACGAGGAAGTGGATGAGATGTACCGGGAGGCACCCAATG
ATAAGAAGGGCAAGTTCAACTAGGTGGCGTTCACCCACATCCTCAAACATGGCTCCAACGACAAAGACGAC

Alignment

ORF - retro_cjac_3743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.8 %
• Parental protein coverage: 91.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYLEGMMSEAPGPINFTM
          Q...SNVFAMFDQ..IQEFKEAFNMIDQN..GF..K.DL.D.LA.LGKNP..EYLE...S.AP.PIN.T.
Retrocopy QSSPSNVFAMFDQFHIQEFKEAFNMIDQNCEGFVHKGDLKDKLA*LGKNPKNEYLESIISKAPRPINLTT

Parental  FLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVDEMYREAPIDKKGNFN
          FLTMFG.KLNG.DP.DVI.NAFACF..EASGF.HEDHL.ELLTTMGD.FTDEEVDEMYREAP.DKKG.FN
Retrocopy FLTMFGKKLNGRDPKDVIQNAFACFN*EASGFFHEDHLWELLTTMGDSFTDEEVDEMYREAPNDKKGKFN

Parental  YVEFTRILKHGAKDKDD
          .V.FT.ILKHG..DKDD
Retrocopy *VAFTHILKHGSNDKDD

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	38.61 RPM
SRP051959_heart	0.02 RPM	97.23 RPM
SRP051959_kidney	0.00 RPM	15.00 RPM
SRP051959_liver	0.00 RPM	3.25 RPM
SRP051959_lung	0.03 RPM	21.73 RPM
SRP051959_lymph_node	0.00 RPM	6.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	10.70 RPM
SRP051959_spleen	0.00 RPM	15.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3743 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3743 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3743 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008540	3 retrocopies	retro_cfam_1384, retro_cfam_2066, retro_cfam_2071,
Callithrix jacchus	ENSCJAG00000012890	4 retrocopies	retro_cjac_3193, retro_cjac_3195, retro_cjac_3743 , retro_cjac_637,
Callithrix jacchus	ENSCJAG00000038151	2 retrocopies	retro_cjac_1279, retro_cjac_3119,
Equus caballus	ENSECAG00000007545	1 retrocopy	retro_ecab_923,
Homo sapiens	ENSG00000101335	1 retrocopy	retro_hsap_956,
Gorilla gorilla	ENSGGOG00000024477	1 retrocopy	retro_ggor_770,
Myotis lucifugus	ENSMLUG00000000207	2 retrocopies	retro_mluc_2534, retro_mluc_327,
Nomascus leucogenys	ENSNLEG00000006109	1 retrocopy	retro_nleu_2460,
Pongo abelii	ENSPPYG00000010971	1 retrocopy	retro_pabe_972,
Pan troglodytes	ENSPTRG00000013458	1 retrocopy	retro_ptro_662,