RetrogeneDB ID: retro_mdom_1346

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:94232605..94233350(-)
• Located in intron of: ENSMODG00000018493

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018480
• Aliases: None
• Description: None

Sequence

>retro_mdom_1346
GTAAACAACAGAAATAGAAAAAAGAAATCACAATTGACAGCTTCTATCCAGGCAATGAAGAAAGAGCAAATGAAACAGAG
AAGGATCAAGGAACACCAAGCAAAAACAAAGAAACTCCAGTGATTGGACACAGGCTTTGGAAGAACTCAAAATACAATTC
AAAAAATAATTAGAGGCTGAAGAGAACTGGGAAAAGAACTTAAAAAGCAAAATAAGTCATCTGGAAACAGAAAATAGTGT
CTTGAAAGACAAAATTAATCAGCTTGAAAATGAGGCAAAGGAGATGAAAGATGTCCTCCAAAGAAAATCGGACTAGAAGG
AGAAGGATGACCAAAGAGCCAGGGATGAAATTCAGTCTTTAAAAACTAGAATACAACAACTAGAAGAAAACGACTTCACA
AGGAAGCAGGAAACTATAAAACAAATTCAAAGAATGAAAAAATTGAGGAAAATATGAAACATCTCATCCATAAAACAGAA
GATTTAGAAAAACCAAGAAAACTCCCCCGACATTCTGGAGCAAGAGAGAAAAGGGGAGATTGAAAGAATCCACAGATCAC
CTCCTGTACTTAATCCCCAACTGACAACACCCAGGAATGTTATTGCCAAATTCAAGAACTACCAGACCAAGGAAAAAATA
TTACAAGCTGCTAAGAAGTCATTCAGATACCATGGAACTATAGTTAGGATAACACAGGATCTGGCTGCATCTACACTGAA
GGACCAAATGGCATGGAATGATATT

Alignment

ORF - retro_mdom_1346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.51 %
• Parental protein coverage: 75.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNPKDKKGTNTLSRAQKNLLEQSKRKQR-GRTQQRKKSEIPGNWIQALEELKMQSKTQLREAEDNWEKNL
          .N....K....L..A..........KQR.G......K......W.QALEELK.Q.K..L.EAE.NWEKNL
Retrocopy VNNRNRKKKSQLT-ASIQAMKKEQMKQR>GSRNTKQKQRNSSDWTQALEELKIQFKK*L-EAEENWEKNL

Parental  KTKISHLETENSVLKAKINQLENEAKEMKDEAKQMKDEVKKMKDDLQRKSDQKENMKHLIHKTEDLENRS
          K.KISHLETENSVLK.KINQLENEAKEMKD......D...K.KDD.QR..D.....K..I...E......
Retrocopy KSKISHLETENSVLKDKINQLENEAKEMKDVLQRKSD*--KEKDD-QRARDEIQSLKTRIQQLEENDFTR

Parental  RRDNLRIIGLPEDHDKRKSLDIILQEIIK--ENCPKILEQEGKVETDRIHRSPPVLNPQLTTPRNVIAKF
          .......I.......K......I.Q.I.K..EN.P.ILEQE.K.E..RIHRSPPVLNPQLTTPRNVIAKF
Retrocopy KQETIKQIQRMKKLRKI*NISSIKQKI*KNQENSPDILEQERKGEIERIHRSPPVLNPQLTTPRNVIAKF

Parental  KDYQ----ILQAAKKKSLRYQGTTVRITQDLAASTLKKRKAWNTI
          K.YQ....ILQAA.KKS.RY.GT.VRITQDLAASTLK...AWN.I
Retrocopy KNYQTKEKILQAA-KKSFRYHGTIVRITQDLAASTLKDQMAWNDI

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_1346 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1346 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018480	3 retrocopies	retro_mdom_1071, retro_mdom_1072, retro_mdom_1346 ,