RetrogeneDB ID: retro_mdom_1600

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:123453292..123453708(+)
• Located in intron of: ENSMODG00000007685

Retrocopy information

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

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_1600
CACAAGCTAATAACCAGTTGCCACTACCAAGTGCTTCACAAAGAATATAATTCAGAATCACCTGCTCCTGAGCCACTGAC
ACCTTCAATACAGCACAGGCTTCTCCTTCTGCCCCTATACTTGAACCAAATGTATTTCTCCTCTACTTTAAAAGCAGTAT
GAACAAGGAAGCAACTGCAACTTCAGAAAGGGAAACAGAGAGTTTTATCTTGTGCTGCCAACCCTACATCAGTTTCCTCT
CTTCTAAGGATGAGGAAGCAAGGAAGGCCAAAACAGCTGCAATGGCAGCTGCTACAGCAGGAGCACTCCTAGGAAAAAAG
ACTTTCCTCCAAAAACTGATTTTAGTGATGCAGATTAGCTTAGAGTGGGTGATCATTTTAATCTTCATGCTAGTGTTATT
CATGGAATTAATTTTC

Alignment

ORF - retro_mdom_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.68 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HKPMTTRRYQVLHNEDDNSELPVVEPPSTST-QIPQTSPSAPILEPETSPPPYSS-ITVEAAATSEPETH
          HK..T...YQVLH.E..NSE.P..E.P.T......Q.SPSAPILEP........S....EA.ATSE.ET.
Retrocopy HKLITSCHYQVLHKEY-NSESPAPE-PLTPS<NTAQASPSAPILEPNVFLLYFKSSMNKEATATSERETE

Parental  SEFYPVPPPYSVATSLPTYDEAEKAKAAAMAAAAAEPSL-REEEFPPRDDFSDADQLRVGNDG-IFMLAF
          S......P..S...S.....EA.KAK.AAMAAA.A...L.R...FPP..DFSDAD.LRVG....IFML..
Retrocopy SFILCCQPYISFLSSKD--EEARKAKTAAMAAATAGALL<RKKDFPPKTDFSDAD*LRVGDHF>IFMLVL

Parental  FMAFIF
          FM..IF
Retrocopy FMELIF

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_1600 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1600 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,