RetrogeneDB ID: retro_pabe_972

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12_random:9814704..9815173(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL9
• Ensembl ID: ENSPPYG00000010971
• Aliases: None
• Description: Myosin regulatory light polypeptide 9 [Source:UniProtKB/Swiss-Prot;Acc:Q5RBA4]

Sequence

>retro_pabe_972
CAGGGGGCCACATCCAATGTCTTCGTGATGTTCGACCAGTTCCATATCCAGGAGTTTAAGGAGGCTTTCAACATGATTGA
CCAGAACCATGATGGCTTCACTGACAAGGGGGACAGCACGACAAGCTGGCTTCACTGCAGAAGAACCCCAAGGATGAATA
CCTGCAGGGCATGATGAGCGAGCCCCAGGGGCCCATCAACTTCACCACTTCCCTCACCATGTTTGGGGAGAAGCTGAATG
GAACAGACCCCCAGGATGTGATCCAAAACGCCTTCACCTGCTTCAGTGAGGAATCCTCAGGTTTCATTCATGAGGACCAC
CTCCAGGAGCTGCTCACCACCATGGGTGACAGCTTCACAGATGAGGAAGTGGATGAGATGTACTGGGAGGCGCCCATTGA
TAAAAAAGGCAAGTTCAACTAGGTGGAGTTCACCTGCGTCCCAAACATGGCGCCAAGGGCAAAGATGAC

Alignment

ORF - retro_pabe_972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• 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.DGF.DK.D..HD.LASL.KNP.DEYL.GMMSE..GPINFT
Retrocopy QGATSNVFVMFDQFHIQEFKEAFNMIDQNHDGFTDKGDS<HDKLASLQKNPKDEYLQGMMSEPQGPINFT

Parental  MFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVDEMYREAPIDKKGNF
          ..LTMFGEKLNGTDP.DVI.NAF.CF.EE.SGFIHEDHL.ELLTTMGD.FTDEEVDEMY.EAPIDKKG.F
Retrocopy TSLTMFGEKLNGTDPQDVIQNAFTCFSEESSGFIHEDHLQELLTTMGDSFTDEEVDEMYWEAPIDKKGKF

Parental  NYVEFTRI-LKHGAKDKDD
          N.VEFT....KHGAK.KDD
Retrocopy N*VEFTCV<PKHGAKGKDD

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	68.23 RPM
SRP007412_cerebellum	0.00 RPM	6.93 RPM
SRP007412_heart	0.00 RPM	254.95 RPM
SRP007412_kidney	0.00 RPM	98.41 RPM
SRP007412_liver	0.00 RPM	40.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_972 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 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	ENSPPYG00000009032	3 retrocopies	retro_pabe_1236, retro_pabe_2585, retro_pabe_3026,
Pongo abelii	ENSPPYG00000010971	1 retrocopy	retro_pabe_972 ,
Pan troglodytes	ENSPTRG00000013458	1 retrocopy	retro_ptro_662,