RetrogeneDB ID: retro_cjac_3193

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:20255804..20256319(+)
• Located in intron of: ENSCJAG00000018988

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_3193
ATGTCCAGCAAGTGGGCCAAAGCCAAGACCACCACGAAGCGGGCAGAGCAGGCCACATCCAATGTCTTCGCGATGTTTGA
CCAGTTCCACATCCAGGAGTTCAAGGAGGCTTTCAACATGATTGACCAGAACTGTGAAGGCTTCGTTCACAAGGGGGACC
TGAAGGAAAACCTGGCCTGACTGGGGAAGAACCCCAAGAATGAATACCTGGAGAGTATAATAAGCAAGGCCCCGAGGCCC
ATCAACTTCACCACTTTCCTCACCATGTTTGGGAAGAAGCTGAACGGCAGGGACCCCAAGGATGTGATCCAAAACGCCTT
TGCCTGCTTCAATTAGGAAGCCTCAGGTTTCTTCCATGAGGACCACCTCTGGGAGCTGCTCACCACCATGGGTGACAGCT
TCACAGACGAGGAAGTGGATGAGATGTACCGGGAGGCACCCAATGATAAGAAGGGCAAGTTCACTAGGTGGCGTTCACCC
ACATCCTGAAACATGGCTCCAACAACAAAGACGAC

Alignment

ORF - retro_cjac_3193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKRAKAKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYL
          MSSK.AKAKTT.KR...ATSNVFAMFDQ..IQEFKEAFNMIDQN..GF..K.DL...LA.LGKNP..EYL
Retrocopy MSSKWAKAKTTTKRAEQATSNVFAMFDQFHIQEFKEAFNMIDQNCEGFVHKGDLKENLA*LGKNPKNEYL

Parental  EGMMSEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVD
          E...S.AP.PINFT.FLTMFG.KLNG.DP.DVI.NAFACF..EASGF.HEDHL.ELLTTMGD.FTDEEVD
Retrocopy ESIISKAPRPINFTTFLTMFGKKLNGRDPKDVIQNAFACFN*EASGFFHEDHLWELLTTMGDSFTDEEVD

Parental  EMYREAPIDKKGNFNY-VEFTRILKHGAKDKDD
          EMYREAP.DKKG.F...V.FT.ILKHG...KDD
Retrocopy EMYREAPNDKKGKFTR<VAFTHILKHGSNNKDD

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	0.05 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_3193 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3193 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,