RetrogeneDB ID: retro_cjac_637

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:172796008..172796422(-)
• 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_637
AAGGAGGCTTTCAACATGATCAACCAGAACCGTGATGGCTTCAGTGACAAGGAGGACCTGCACGACATGCTGGCCTCGCT
GGGGAAGAACCCTACAGACGAATACCTGGAGGGCATGATGATCGAGGCCCCAGGGCCCATCAACTTCACCATGTTCCTCA
CCATGTTTGGGGAGAAGCTCAATGGCACAGACCCCGAGGACGTGATCTGCAATGCCTTTGCCCGCTTCGCCGAATAAGCC
TCAGGTTTCATCCATGAGGACCACCTCCTGGAGCTGCTGACCACCATGGGTGATCGCTTCATAGATGAGGAAATGGACGA
GATGTACCGGGAGGCACCCACTGACAAGAAAGGCAACTTCAACCATGTGGAGTTCACCCGCATCATCAAACATGGTGCCC
AGGACAAAGACGAT

Alignment

ORF - retro_cjac_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 80.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYLEGMMSEAPGPINFTMFLTMFGEKLNGTDPEDVIR
          KEAFNMI.QNRDGF.DKEDLHDMLASLGKNPTDEYLEGMM.EAPGPINFTMFLTMFGEKLNGTDPEDVI.
Retrocopy KEAFNMINQNRDGFSDKEDLHDMLASLGKNPTDEYLEGMMIEAPGPINFTMFLTMFGEKLNGTDPEDVIC

Parental  NAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVDEMYREAPIDKKGNFNYVEFTRILKHGAKDKDD
          NAFA.F.E.ASGFIHEDHL.ELLTTMGDRF.DEE.DEMYREAP.DKKGNFN.VEFTRI.KHGA.DKDD
Retrocopy NAFARFAE*ASGFIHEDHLLELLTTMGDRFIDEEMDEMYREAPTDKKGNFNHVEFTRIIKHGAQDKDD

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	0.04 RPM	38.61 RPM
SRP051959_heart	0.28 RPM	97.23 RPM
SRP051959_kidney	0.13 RPM	15.00 RPM
SRP051959_liver	0.26 RPM	3.25 RPM
SRP051959_lung	0.29 RPM	21.73 RPM
SRP051959_lymph_node	0.41 RPM	6.21 RPM
SRP051959_skeletal_muscle	0.22 RPM	10.70 RPM
SRP051959_spleen	0.32 RPM	15.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_637 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_637 has 0 orthologous retrocopies within eutheria group .

---

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,