RetrogeneDB ID: retro_ptro_1006

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:39567776..39568279(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL12B
• Ensembl ID: ENSPTRG00000009836
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827]

Sequence

>retro_ptro_1006
ATGTCGAGCAAAAAGGCAAAGACGAAGACCACCAAGAAATGCCCTCAGTGCACAATATCCAATGTGTTTGCCATGTTTGA
CCAGTCACAGATTCAGGAGTTCAAAGAGGCCTTCAACATGATTGATTAGAACAGAGATGGTTTCATCAACAAGGAAGATT
TGCATGATATGCTTGCTTCTCTAGGGAAGAATCCCACTGATGCATACCTTGATGCCACGATGAATGAGGCACCAGGGCCC
ATTAATTTCACTATGTTTGGTGAGAAGTTAAATGGCACAGATCTGAAGATGTCATCAGAAATGCTTCTGCTTGCTTTGAT
GAAGAAGCAACAGGCACCATTCAGGAAGATTACCTGAGAGAGCTGATGACAACCATGGGGGATCAGTTTACAGATGAGGA
AGTGGATGAGCTGCACAGAGAAGCACCTATTGACAAAAAGGGAAATTTCAATTACATCGAGTTCACAAGCATCCTGAAAC
ATGGAGTAAAAGACAAAGATGAC

Alignment

ORF - retro_ptro_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDAYL
          MSSKKAKTKTTKK.PQ...SNVFAMFDQSQIQEFKEAFNMID.NRDGFI.KEDLHDMLASLGKNPTDAYL
Retrocopy MSSKKAKTKTTKKCPQCTISNVFAMFDQSQIQEFKEAFNMID*NRDGFINKEDLHDMLASLGKNPTDAYL

Parental  DAMMNEAPGPINFTMFLTMFGEKLNGTD-PEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEV
          DA.MNEAPGPINFTMF....GEKLNGTD..EDVIRNA.ACFDEEATGTIQEDYLREL.TTMGD.FTDEEV
Retrocopy DATMNEAPGPINFTMF----GEKLNGTD<SEDVIRNASACFDEEATGTIQEDYLRELMTTMGDQFTDEEV

Parental  DELYREAPIDKKGNFNYIEFTRILKHGAKDKDD
          DEL.REAPIDKKGNFNYIEFT.ILKHG.KDKDD
Retrocopy DELHREAPIDKKGNFNYIEFTSILKHGVKDKDD

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	0.66 RPM	78.40 RPM
SRP007412_cerebellum	0.61 RPM	74.53 RPM
SRP007412_heart	0.09 RPM	98.02 RPM
SRP007412_kidney	0.08 RPM	209.79 RPM
SRP007412_liver	0.07 RPM	115.52 RPM
SRP007412_testis	0.32 RPM	92.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1006 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1006 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1487
Gorilla gorilla	retro_ggor_1140

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012665	1 retrocopy	retro_amel_1847,
Canis familiaris	ENSCAFG00000032168	1 retrocopy	retro_cfam_1224,
Dasypus novemcinctus	ENSDNOG00000007004	2 retrocopies	retro_dnov_463, retro_dnov_953,
Dipodomys ordii	ENSDORG00000007562	1 retrocopy	retro_dord_531,
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311,
Felis catus	ENSFCAG00000022871	1 retrocopy	retro_fcat_2019,
Homo sapiens	ENSG00000118680	4 retrocopies	retro_hsap_1487, retro_hsap_3129, retro_hsap_3451, retro_hsap_3985,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Myotis lucifugus	ENSMLUG00000005189	2 retrocopies	retro_mluc_706, retro_mluc_947,
Monodelphis domestica	ENSMODG00000021464	1 retrocopy	retro_mdom_987,
Mustela putorius furo	ENSMPUG00000005011	1 retrocopy	retro_mputfur_294,
Mus musculus	ENSMUSG00000034868	2 retrocopies	retro_mmus_1483, retro_mmus_1539,
Nomascus leucogenys	ENSNLEG00000006907	3 retrocopies	retro_nleu_1709, retro_nleu_1906, retro_nleu_2250,
Otolemur garnettii	ENSOGAG00000029777	2 retrocopies	retro_ogar_2409, retro_ogar_857,
Pongo abelii	ENSPPYG00000009032	3 retrocopies	retro_pabe_1236, retro_pabe_2585, retro_pabe_3026,
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,
Rattus norvegicus	ENSRNOG00000015733	2 retrocopies	retro_rnor_1614, retro_rnor_2718,
Tarsius syrichta	ENSTSYG00000010418	9 retrocopies	retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,