RetrogeneDB ID: retro_mdom_987

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:128927451..128927901(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL12B
• Ensembl ID: ENSMODG00000021464
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827]

Sequence

>retro_mdom_987
ATGTATTTGCTATTTGATCAATCAAAAATTCAGAAATTCAAAGAGGCCTTCAATATGATTTATAAGAACAGAGACAGTTT
CATTGACAAGGAATATTTATGTGACATGTTTGCTTCTTTAGGAAACAATCCAACTGATGAGTAACTAGATGCCGTGATGA
ATGAAGCTTCAGGTCCTATAAATTTTACCATGTTCCTAGCAATGTTTGGGGAAAAGTTAAATGGAACTGATCCAGAAGAT
GTCATCAGAAGTGCTTTTGCTTGCTTTGATTAAGAAGCTATCAAAACTATTCAAGATTACTTGAGAGAATTACTGACAAC
AATGGGAGATAGATTCACAGATGAAGAAGTAGATGAACTATATAAAGAAGCACCTATTGACAAAAAGGGAAATTTCAATT
ATATTGAGTTCGCACACATTCTTAATCATGGAGTAAAAGACAAAGATGAC

Alignment

ORF - retro_mdom_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.46 %
• Parental protein coverage: 87.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDAYLDAMMNEAPGPINFTMFLTMFG
          ....FDQS.IQ.FKEAFNMI..NRD.FIDKE.L.DM.ASLG.NPTD..LDA.MNEA.GPINFTMFL.MFG
Retrocopy MYLLFDQSKIQKFKEAFNMIYKNRDSFIDKEYLCDMFASLGNNPTDE*LDAVMNEASGPINFTMFLAMFG

Parental  EKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEVDELYREAPIDKKGNFNYIEFTR
          EKLNGTDPEDVIR.AFACFD.EA..TIQ.DYLRELLTTMGDRFTDEEVDELY.EAPIDKKGNFNYIEF..
Retrocopy EKLNGTDPEDVIRSAFACFD*EAIKTIQ-DYLRELLTTMGDRFTDEEVDELYKEAPIDKKGNFNYIEFAH

Parental  ILKHGAKDKDD
          IL.HG.KDKDD
Retrocopy ILNHGVKDKDD

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	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_987 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_987 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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	ENSMODG00000001476	1 retrocopy	retro_mdom_1246,
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,
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,