RetrogeneDB ID: retro_mdom_1391

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:268518521..268518746(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC2L
• Ensembl ID: ENSMODG00000003889
• Aliases: None
• Description: trafficking protein particle complex 2-like [Source:HGNC Symbol;Acc:30887]

Sequence

>retro_mdom_1391
GATAACAGGGTATATTCTATGCAACGAATCCTAAGATTAAATTTGTTAGGGTGTTAAATTCCTCCAATACAGCTCTTTGA
GAAAGCTGAGATCTGCATTATGTTTTGAAAGTTGCTACATAATTCTTATGCAGATGTTGTGTACAATCCTTCCTAGAATC
CTGGAGTCTATATTCATTATAGAGCCTTTGACAATATGATGACTTCGATGATGGTTCAGGTTTGT

Alignment

ORF - retro_mdom_1391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.94 %
• Parental protein coverage: 53.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DYKVYG-YVTNSKVKFVMVVDSSNTALRDN-EIRSMFRKL-HNSYTDVMCNPFYNPGDRIHSRAFDNMVT
          D..VY..Y.TN.K.KFV.V..SSNTAL....EI..MF.KL.HNSY.DV..NP..NPG..IH.RAFDNM.T
Retrocopy DNRVYS<YATNPKIKFVRVLNSSNTAL*ES>EICIMF*KLLHNSYADVVYNPS*NPGVYIHYRAFDNMMT

Parental  SMMVQVC
          SMMVQVC
Retrocopy SMMVQVC

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_1391 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1391 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 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000003547	1 retrocopy	retro_etel_1888,
Homo sapiens	ENSG00000167515	1 retrocopy	retro_hsap_4852,
Monodelphis domestica	ENSMODG00000003889	2 retrocopies	retro_mdom_1165, retro_mdom_1391 ,
Rattus norvegicus	ENSRNOG00000014581	3 retrocopies	retro_rnor_1444, retro_rnor_1866, retro_rnor_2239,