RetrogeneDB ID: retro_mdom_665

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:745155428..745155899(-)
• Located in intron of: ENSMODG00000010275

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000004795
• Aliases: None
• Description: None

Sequence

>retro_mdom_665
ATTCCTAAGCAGTCAGAAGTTGAAGACTGGAGCTCCTGGGAGCTCCACACAAGTATAAAGATTGAAGGAGGCCATGGAAA
CGGGACAGCACAACAACATCCACTGGAACAAGTAGAACCTGACTATGTTAAAGACATGGCACCAACTATAAGGAAAACAC
AAGAAATTATTATTAAGAAGAGAACCACTAGATTTTGGCACTCCAGATGGCGCCACAGGTTTCTCTATAGATGAGCAGCT
ACACAAGATATTCCTTTCATTCACCAATCTCCTGAATTGGGTGACTTGGCTACCTGGCAGGAGAATACAAATGCATGGGA
AGAAGATGCAGCCTGGCAAGCAGAGGAAGTCCCGAGATAGCAGAAAATAGCTGACAGAGAAAAGAGGGCAGCGGAACAAC
AAAGGAAGAAAATGGAAAAGGAAGCACAATGACTAATGAAGAAAGAACAGAATAAAATCGGTGTGAAACTG

Alignment

ORF - retro_mdom_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.32 %
• Parental protein coverage: 76.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPKQSEVEDWSSWDEDAPTSIKIEGGNGNGTAQQNTLEQIEPDYFKDMAPTIRKTQ-KIIIKKREPLNFG
          .PKQSEVEDWSSW.....TSIKIEGG.GNGTAQQ..LEQ.EPDY.KDMAPTIRKTQ.K.....REPL.FG
Retrocopy IPKQSEVEDWSSWE--LHTSIKIEGGHGNGTAQQHPLEQVEPDYVKDMAPTIRKTQ>KLLLR-REPLDFG

Parental  IPDGTTGFSS-RLAATQDIPFIHQSPELGDLDTWQENTNAWEEEEDAAWQAEEVLRQQKIADREKRAAEQ
          .PDG.TGFS..R.AATQDIPFIHQSPELGDL.TWQENTNAWEE..DAAWQAEEV.R.QKIADREKRAAEQ
Retrocopy TPDGATGFSI<R*AATQDIPFIHQSPELGDLATWQENTNAWEE--DAAWQAEEVPR*QKIADREKRAAEQ

Parental  QRKKMEKEAQRLMKKEQNKIGVKL
          QRKKMEKEAQ.LMKKEQNKIGVKL
Retrocopy QRKKMEKEAQ*LMKKEQNKIGVKL

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_665 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_665 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 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dasypus novemcinctus	ENSDNOG00000007465	2 retrocopies	retro_dnov_1014, retro_dnov_2449,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665 ,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Pongo abelii	ENSPPYG00000018824	1 retrocopy	retro_pabe_622,
Pan troglodytes	ENSPTRG00000020513	1 retrocopy	retro_ptro_515,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,