RetrogeneDB ID: retro_ptro_662

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:8103713..8104184(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL9
• Ensembl ID: ENSPTRG00000013458
• Aliases: None
• Description: None

Sequence

>retro_ptro_662
CAGGGGGCCACATCCAATGTCTTTGTGATGTTCGACCAGTTCCACATCCAGGAGTTTAAGGAGGCTTTCAACATGATTGA
CCAGAACCATGATGGCTTCATTGACAAGGGGGACAGCACGACATGCTGGCTTCACCACGGAAGAACCCCATGGATGAATA
CCTGCAGGGCATGATGAGCGAGGCCCCAGGGCCCATCAACTTCACCACTTCCCTCACCATGTTTGGGGAGAAGCTGAATG
GAACAGACCCCCAGGATGTGATCCAAAACGGCTTCACCTGCTTCAACGAGGAATCCTCAGGTTTCATTCATGAGGACCAC
CTCCAGGAGCTGCTCACCACCATGGGTGACAGCTTCACAGATGAAGAAGTGGATGAGATGTACTGGGAGGCACCCATTGA
TAAAAAAAGACAAGTTCAACTAGGTGGAGTTCACCTGCATCCTCATACATGGTGCCAAGGGCAAAGATGAC

Alignment

ORF - retro_ptro_662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.13 %
• Parental protein coverage: 91.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDL-HDMLASLGKNPTDEYLEGMMSEAPGPINFT
          Q.ATSNVF.MFDQ..IQEFKEAFNMIDQN.DGFIDK.D..HDMLAS..KNP.DEYL.GMMSEAPGPINFT
Retrocopy QGATSNVFVMFDQFHIQEFKEAFNMIDQNHDGFIDKGDS<HDMLASPRKNPMDEYLQGMMSEAPGPINFT

Parental  MFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVDEMYREAPID-KKGN
          ..LTMFGEKLNGTDP.DVI.N.F.CF.EE.SGFIHEDHL.ELLTTMGD.FTDEEVDEMY.EAPID.KK..
Retrocopy TSLTMFGEKLNGTDPQDVIQNGFTCFNEESSGFIHEDHLQELLTTMGDSFTDEEVDEMYWEAPID>KKDK

Parental  FNYVEFTRILKHGAKDKDD
          FN.VEFT.IL.HGAK.KDD
Retrocopy FN*VEFTCILIHGAKGKDD

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	24.74 RPM
SRP007412_cerebellum	0.00 RPM	7.53 RPM
SRP007412_heart	0.03 RPM	529.00 RPM
SRP007412_kidney	0.03 RPM	129.95 RPM
SRP007412_liver	0.07 RPM	28.28 RPM
SRP007412_testis	0.32 RPM	33.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_662 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_662 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_956

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 19 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,
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	ENSPTRG00000009836	4 retrocopies	retro_ptro_1006, retro_ptro_2118, retro_ptro_2340, retro_ptro_2705,
Pan troglodytes	ENSPTRG00000013458	1 retrocopy	retro_ptro_662 ,