RetrogeneDB ID: retro_mdom_48

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:209361261..209362020(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024262
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NDFIP2
• Ensembl ID: ENSMODG00000001586
• Aliases: None
• Description: Nedd4 family interacting protein 2 [Source:HGNC Symbol;Acc:18537]

Sequence

>retro_mdom_48
ATGGATCTTCACTCTTCCGTGACCGGCTACTATCAAGTGCTTCGCAATGAGGAAAATCATACGGAATCCCCGGCCGTGGA
GCAGCCTTCCACGTCCATGCAGATTACACTCCTGACAGCACCCCAGAGGACTACTTCGCCGCCTGCCCCTGCACTGACAT
TCCCAGATTTGGGCGCCTCCCCTCTACCCTATGGCCGGGGCCCCCTGGAGGCCTCGACCACCTCTGAAACCGAATGTCCC
TGTGAGCTCTACCCAGTGCCACCACCCTATAGTGTCGCCACATCCCTTCCCACATACGATGAGGCTGAGAGGGCCAAAGC
AGCGGCCTTGGCTGCCAGTGCCGCCCCCTCTGGAGAGCCCACCCAGAGAGAAAACGACTTCCCTTCCAGGGAGGACTCAA
CCTCCAATGACTCTGAGCAGCTACGAGTGGGCAATGATGGCGTCTTCATGGTGGCCTTCTTCATGGCCTTCATCTTCAAC
TGGATTGGATTTTGCTTATCCTTCTGTACAACCAACTCCATAGCCGGGAGATATGGTGCCCTCTGTGGATTTGGCCTTTC
CTTGACCAAGTGGATCCTCATCGTCAGGTTTTCAGATTACTTTACAGGATACTTCAATGGACAGTACTGGCTTTGGTGGA
TATTTCTTTTAATTGGCCTCTTGCTTTTCTTCAGAGGATTTTACAGTTACCTGAAAGTCAGGAACATTTCAGAAAGACTG
GATACTACCCATAGAACAAGATACATCTTCTCAAGTTAA

Alignment

ORF - retro_mdom_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 92.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HNEDDNSELPVVEPPSTSTQIPQ--TSPSAPILE-PE--TSPPPYSSITVEAAATSEPETHSEFYPVPPP
          H.E....E.P......T....PQ..TSP.AP.L..P....SP.PY.....EA..TSE.E...E.YPVPPP
Retrocopy HTESPAVEQPSTSMQITLLTAPQRTTSPPAPALTFPDLGASPLPYGRGPLEASTTSETECPCELYPVPPP

Parental  YSVATSLPTYDEAEKAKAAAMAAAAA---EPSLREEEFPPRDDFS--DADQLRVGNDGIFMLAFFMAFIF
          YSVATSLPTYDEAE.AKAAA.AA.AA...EP..RE..FP.R.D....D..QLRVGNDG.FM.AFFMAFIF
Retrocopy YSVATSLPTYDEAERAKAAALAASAAPSGEPTQRENDFPSREDSTSNDSEQLRVGNDGVFMVAFFMAFIF

Parental  NWIGFCLSFCITNTIAGRYGAICGFGLSLIKWILIVRFSDFFTGYVNGQYWLWWIFLVLGLLLFFRGFVN
          NWIGFCLSFC.TN.IAGRYGA.CGFGLSL.KWILIVRFSD.FTGY.NGQYWLWWIFL..GLLLFFRGF..
Retrocopy NWIGFCLSFCTTNSIAGRYGALCGFGLSLTKWILIVRFSDYFTGYFNGQYWLWWIFLLIGLLLFFRGFYS

Parental  YLKVRNMSESMAAAHRTRFFF
          YLKVRN.SE.....HRTR..F
Retrocopy YLKVRNISERLDTTHRTRYIF

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_48 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_48 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021282	2 retrocopies	retro_cjac_2643, retro_cjac_2644,
Cavia porcellus	ENSCPOG00000014687	1 retrocopy	retro_cpor_753,
Loxodonta africana	ENSLAFG00000000864	1 retrocopy	retro_lafr_841,
Monodelphis domestica	ENSMODG00000001586	2 retrocopies	retro_mdom_1600, retro_mdom_48 ,
Mustela putorius furo	ENSMPUG00000003366	1 retrocopy	retro_mputfur_1079,
Tupaia belangeri	ENSTBEG00000005780	1 retrocopy	retro_tbel_3231,