RetrogeneDB ID: retro_mdom_340

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:213469893..213470837(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008225
• Aliases: None
• Description: None

Sequence

>retro_mdom_340
ACATTTCTGAAAGCCATGGAAGATGGAGGTGTCAAGGTTTTAAAAGAAAGATTAGAAAAATGTTTTTCACCGGTATTTGC
AAACCCTGCATCTACAATCATGTGACCTACTTGACATTTTTGGTGGAATCAGCTTTTTCCCATTGGATAAAATGACTTAC
TTGAAAATCCAGTCCTTTATAAATAAGATGGAAGAAAGCTTGAATATAGTTAAATATACTGCCTTTCTCTATAATGATCA
ACTCATCTGGAGTGGATTAGAGCAAGATGACATGAGAATTTTATATAAATACCTTACTAGTTCTCTATTTCCAAGACACA
TCGAGCCTGAGTTGGCAGGAAGGGATTCACCAATCTGAGCAGAAATGCCAGAAAATCTTCAACATTATGGAAGATTTCTT
ACTGGGCCCTTGAACCTTAATGATCCAGAAGCAAAATGCAGATTTCCCAAAATTTTTGTAAATACAGATGATACTTATGA
AGAGCTTCATTTAATTGTTTATAAGGCCATGAGTGCAGCAGTTTGTTTCATGATTGATGCCTCTATGCAGCCTTCTTTGG
ACTTTTGCCGAAGATTAGACAGCATCGTTGGACCTCAGCTCACAGTTTTAGCATCTGATATTTGTGAACAGTACAACATC
AACAAAAGAATATCAGGATCTGAAAAGGAACCCCAGTTTAAGTTTATCTACTTCAATCATATGAATTTAGCAGAGAAAAG
TACAATTCACATGAGGAAAACACCTAGCATATCACTTACATCTGTTCATCCTGACCTTATGAAGATTCTAGGTGATATCA
ACAGTGATTTTACAAGAATGGATGAAGATGAGGAAATCATCGTGAAGGCAATGAGTGACTATTGGGTTGTTGGGAAAAAA
TCTGATCAGCGAGAACTGTATGTTATTTTGAATAAAAAAAAATGCAAACCTGATTGAGGTCAAT

Alignment

ORF - retro_mdom_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.15 %
• Parental protein coverage: 71.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFLKAMEDGGVKVLKERLEK-FFHRYLQTLHLQSCDLLDIFGGISFFPLDKMTYLKIQSFINKMEESLNI
          TFLKAMEDGGVKVLKERLEK..FHRYLQTLHLQSCDLLDIFGGISFFPLDKMTYLKIQSFINKMEESLNI
Retrocopy TFLKAMEDGGVKVLKERLEK>VFHRYLQTLHLQSCDLLDIFGGISFFPLDKMTYLKIQSFINKMEESLNI

Parental  VKYTAFLYNDQLIWSGLEQDDMRILYKYLTTSLFPRHIEPELAGRDSPIRAEMPGNLQHYGRFLTGPLNL
          VKYTAFLYNDQLIWSGLEQDDMRILYKYLT.SLFPRHIEPELAGRDSPI.AEMP.NLQHYGRFLTGPLNL
Retrocopy VKYTAFLYNDQLIWSGLEQDDMRILYKYLTSSLFPRHIEPELAGRDSPI*AEMPENLQHYGRFLTGPLNL

Parental  NDPEAKCRFPKIFVNTDDTYEELHLIVYKAMSAAVCFMIDASMQPSLDFCRRLDSIVGPQLTVLASDICE
          NDPEAKCRFPKIFVNTDDTYEELHLIVYKAMSAAVCFMIDASMQPSLDFCRRLDSIVGPQLTVLASDICE
Retrocopy NDPEAKCRFPKIFVNTDDTYEELHLIVYKAMSAAVCFMIDASMQPSLDFCRRLDSIVGPQLTVLASDICE

Parental  QYNINKRISGSEKEPQFKFIYFNHMNLAEKSTIHMRKTPSISLTSVHPDLMKILGDINSDFTRMDEDEEI
          QYNINKRISGSEKEPQFKFIYFNHMNLAEKSTIHMRKTPSISLTSVHPDLMKILGDINSDFTRMDEDEEI
Retrocopy QYNINKRISGSEKEPQFKFIYFNHMNLAEKSTIHMRKTPSISLTSVHPDLMKILGDINSDFTRMDEDEEI

Parental  IVKAMSDYWVVGKKSDQRELYVILN-QKNANLIEVN
          IVKAMSDYWVVGKKSDQRELYVILN....ANLIEVN
Retrocopy IVKAMSDYWVVGKKSDQRELYVILN>XXXANLIEVN

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	0.24 RPM	0.00 RPM
SRP007412_cerebellum	0.65 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	1.51 RPM	0.00 RPM
SRP007412_testis	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_340 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_340 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000008225	1 retrocopy	retro_mdom_340 ,