RetrogeneDB ID: retro_mdom_1490

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:288865..289401(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018053
• Aliases: None
• Description: None

Sequence

>retro_mdom_1490
AGCCAGAGTATCTTCAATCAGGAAGAAAATAACAATTCCGGTTGCTACCCAAGTGCTTATGTCATGACTGGACGTGGTGC
CCTCGTGATGCAGGTAGGTTTCCTGGGTTGCTGTGAGGCATAAAGGAATTAGAGTGCATCTTGGGTTTGTTCTTTGACCC
CTCCTCTTGGTAATTTTTGTTATCAAAATAACTTATTTTTCCCGTGAAGAAAAGGTGATTCATGAGGTTTAGGCATTTTA
TAGGGAAATATAAAACAAGATGAAGAACAAAGAAGCCTTTACGAAACCCTCAAAGCCTTCACCAGGTGCTAGATTTTTGT
GTTTGGTTGCGAGACCAATTGATCTTGGGCATCTGTCCCAACAAAGACATTATCTCATTGCTTATTATGAAGTTTTGCCC
ACAAGCTATTGATAAAATCTGCAACAATAAACTCCATGTCATTGAAACTGTCAGCATAGGAATTGCTTTGGTGATCTTTG
GCATGTTTTTCAGTATAAGTCTATGTTGTACTATCCTAAGGAATCAATAAATGGTC

Alignment

ORF - retro_mdom_1490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 82.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TKSIFDQEDNNNSSFYTGVYILIGAGALMMLVGFLGCCGA-VQESQCM-LGLFF-AFLLVIFAIEIAAAI
          ..SIF.QE.NNNS..Y...Y...G.GAL.M.VGFLGCC.A...E..C..LG......LLVIF.I.....I
Retrocopy SQSIFNQEENNNSGCYPSAYVMTGRGALVMQVGFLGCCEA<IKELECI<LGFVL*PLLLVIFVIK----I

Parental  WGYSHKEEVIREVQAFYKETYRKMKDKE-SPYKDTLKA-IHQALDCCGLTGAPEQFILDICPNKDVISSF
          ...S..E.VI.EV.AFY.E...KMK.KE.S.Y..TLKA..HQ.LD.C.......Q.IL.ICPNKD.IS..
Retrocopy TYFSREEKVIHEV*AFYREI*NKMKNKE<SLY-ETLKA<LHQVLDFC--VWLRDQLILGICPNKDIISLL

Parental  TVKPCPQAIEEIFNNKFHIIGAVGIGIAVVMIFGMIFSMILCCAIRRNREMV
          ..K.CPQAI..I.NNK.H.I..V.IGIA.V.IFGM.FS..LCC.I.RN..MV
Retrocopy IMKFCPQAIDKICNNKLHVIETVSIGIALV-IFGMFFSISLCCTILRNQ*MV

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_1490 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1490 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009313	1 retrocopy	retro_eeur_174,
Felis catus	ENSFCAG00000006863	1 retrocopy	retro_fcat_1098,
Myotis lucifugus	ENSMLUG00000006901	1 retrocopy	retro_mluc_2384,
Monodelphis domestica	ENSMODG00000018053	3 retrocopies	retro_mdom_1490 , retro_mdom_226, retro_mdom_872,
Monodelphis domestica	ENSMODG00000020396	1 retrocopy	retro_mdom_228,
Mus musculus	ENSMUSG00000030342	1 retrocopy	retro_mmus_3022,
Ictidomys tridecemlineatus	ENSSTOG00000001348	1 retrocopy	retro_itri_768,