RetrogeneDB ID: retro_mdom_1165

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:328735894..328736117(-)
• 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_1165
AAAAGGCTTGTGGATCAGAGAGAGTCCTACTAGAATCTTCTGTGTCCCCCCAGAGAAGGCTATCAAATATCTGGCTATGT
AGCACATTCCAAAAGGAAATTTGTTACAATGCTAGGTCCCTCCAGTATAACACTTTGGGATAATAATATGCACAGTATGT
TATAAAGGCTACATAATTCCTATAGTAGGTGTCATACATAACCCCTTCCATAATCCTGGAGAT

Alignment

ORF - retro_mdom_1165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.33 %
• Parental protein coverage: 52.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KALVDQRELYLGLLYPT-EDYKVYGYVTNSKVKFVMVVDSSNTALRDNEIRSMFRKLHNSYT-DVMCNPF
          K.LVDQRE.Y..LL.P..E.Y...GYV..SK.KFV.....S...L.DN...SM...LHNSY...V..NPF
Retrocopy KRLVDQRESY*NLLCPPREGYQISGYVAHSKRKFVTMLGPSSITLWDNNMHSML*RLHNSYS>GVIHNPF

Parental  YNPGD
          .NPGD
Retrocopy HNPGD

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_1165 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1165 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,