RetrogeneDB ID: retro_mdom_67

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:81826175..81827045(+)
• Located in intron of: ENSMODG00000004292

Retrocopy information

• Ensembl ID: ENSMODG00000025078
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GNPDA2
• Ensembl ID: ENSMODG00000020593
• Aliases: None
• Description: glucosamine-6-phosphate deaminase 2 [Source:HGNC Symbol;Acc:21526]

Sequence

>retro_mdom_67
ATGAAACTCATCATCCTGGATAATAAACCTCAGGCCTGTGAATGGGCTGCTAAGTACATCAGAAACCGAATCATCCTGTT
TAGCCCAGGGCCAGACAAGTATTTCACCCTGGGACTTCCCACTGGGAATACCCCTATGGGGTGCTACAAGAAGCTGATTG
AGTATTATAATAACGGAGACCTGTCCTTTAAGTATGTGAAGACATTTAACATGGACGAGTATGTGGGCCTCCCCCGTGAC
CACCCTGAGAGCTACCATTCCTTTATGTGGAACAACCTCTTCAAGCACATTGACATCCACCCCGAAAACACCCACATTCT
GGATGGGAATGCAGCTGATCTGCAGGCTGAATGTGATGCTTATGAAGAGAAGATCAAGGCGGCTGGAGGGATTGAGCTAT
TTCTTGGAGGTATTGGCTACCATGGGCATATTGCCTTCAATGAGCCTGGCTCAAGTCTGGTGTCTAGGACGCGCGTGAAA
ACTCTGGCCATGGATACTATCCTGGCCAATGCTCGGTTCTTTAATGGAGATCTCTCAAAAGTCCCTAAGCTGGCTCTGAC
AGTGGGTGTAGGCACAGTCATGGATGCCAGAGAGGTCATGATCTTAATTACAGGGGCCAAAAAGGCATTTGCACTGTATA
AGGTCACTGAGGAGGGGGTAAGTCACATGTGGACCGTGTCTGCCTTCCAGCAGCATCCCCGTACAATATTCGTGTGTGAT
GAAGATGCCACACTGGAGCTTAAAGTGAAAACTGTCAAGTATTTCAAAGGGTTGATGCTTGTTCATAACAAGCTAGTAGA
ACCACTATACAGTATAAAAGAAAAAGAAACAGAGAAAAGCCAACCTGCCAAGAAGCCATATAGTGACTAA

Alignment

ORF - retro_mdom_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 99.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLVILDNYALASEWAAKYICNRIIQFKPRKDRYFTLGLPTGSTPLGCYKKLIEYHKNGDLSFKYVKTFN
          M.L.ILDN...A.EWAAKYI.NRII.F.P..D.YFTLGLPTG.TP.GCYKKLIEY..NGDLSFKYVKTFN
Retrocopy MKLIILDNKPQACEWAAKYIRNRIILFSPGPDKYFTLGLPTGNTPMGCYKKLIEYYNNGDLSFKYVKTFN

Parental  MDEYVGLPRNHPESYHSYMWNNFFKHIDIDPNNVHILDGNASDLQAECDSFERKIEEAGGIDLFVGGIGP
          MDEYVGLPR.HPESYHS.MWNN.FKHIDI.P.N.HILDGNA.DLQAECD..E.KI..AGGI.LF.GGIG.
Retrocopy MDEYVGLPRDHPESYHSFMWNNLFKHIDIHPENTHILDGNAADLQAECDAYEEKIKAAGGIELFLGGIGY

Parental  DGHIAFNEPGSSLVSRTRLKTLAMDTILANAKYFDGDLSKVPTMALTVGVGTVMDAREVMILITGAHKAF
          .GHIAFNEPGSSLVSRTR.KTLAMDTILANA..F.GDLSKVP..ALTVGVGTVMDAREVMILITGA.KAF
Retrocopy HGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFNGDLSKVPKLALTVGVGTVMDAREVMILITGAKKAF

Parental  ALYKAIEEGVNHMWTVSAFQQHPRTIFVCDEDATLELRVKTVKYFKGLMHVHNKLVDPLYSMKEE
          ALYK..EEGV.HMWTVSAFQQHPRTIFVCDEDATLEL.VKTVKYFKGLM.VHNKLV.PLYS.KE.
Retrocopy ALYKVTEEGVSHMWTVSAFQQHPRTIFVCDEDATLELKVKTVKYFKGLMLVHNKLVEPLYSIKEK

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_67 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_67 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000015385	1 retrocopy	retro_meug_1772,
Monodelphis domestica	ENSMODG00000010398	1 retrocopy	retro_mdom_1337,
Monodelphis domestica	ENSMODG00000020593	1 retrocopy	retro_mdom_67 ,
Sorex araneus	ENSSARG00000004814	1 retrocopy	retro_sara_593,
Tarsius syrichta	ENSTSYG00000010930	1 retrocopy	retro_tsyr_806,
Tursiops truncatus	ENSTTRG00000016022	1 retrocopy	retro_ttru_891,
Vicugna pacos	ENSVPAG00000011080	1 retrocopy	retro_vpac_409,