RetrogeneDB ID: retro_mdom_2021

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:53813711..53814524(-)
• Located in intron of: ENSMODG00000014360

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAQR4
• Ensembl ID: ENSMODG00000016528
• Aliases: None
• Description: progestin and adipoQ receptor family member IV [Source:HGNC Symbol;Acc:26386]

Sequence

>retro_mdom_2021
TCGGGCCCCCGCTTACTGGACTGGATTAACACCCCTTCTCACCTACAGTTCAACCCGTTCATCCTGACAGGATACCGGCC
CGCCAGCAGCGTCTCTGGGTGTGTGCGCAGCCTCTTCTACCTACACAATGAGCTCGGTAACATCTACATCCACGTCCTAG
CCCTCCTGACCTTCTTGGTGATGCTGCCCCTTACCATCCCCTGGGACCAACTGGGCTGGGGCCACTGGCTGGGCTGTACC
CACTTCTTGGCCTGCCTGGCACCCCCTGCTGGCTCTATCCTCTATCACCTCTTCATGTGCCACCGAGGGGGCAACCGAGT
GTACTCCCACCTCCTAGCCCTCGATATGTGCGGGGTCTGGCTGGCCAACAGCCTCGGAGCCATCCCCATGATCCAGTGCA
CCCTGCTCTGCTGGCCTTGCCTGCGCCTGTTCGCCCTGGTGATGTATGCCTTCCTGTCCGTCATGGCTGGTTGGTGGGCC
CTCACTGCTTTGTCCACTACCGCCCGCCTCCAGGCCTTTGGCTGGCAAGCCATCGCCCGCCTGCTGGTATTTGGGATCCG
GTGGCTAGGGTTGGGCACTGGTGCGCCGAGGTCCCTGCTGTGCTATCTCCGAATGGATGCGTTGGCCCTCCTGGGAGGGC
TGGTGAACGTGGCCCGGCTGCCCGAGCGCTGGGGACCCGGGATTTTTGACTATTGGTGCAATTCCCACCAGATCATGCAC
TTCCTGAGTGTGATTTCCATCCTACAGATGCATGCAGGGGTCATTCCAGATCTTGTCTGGGCTGCTAGCCATGATTATGC
CTGCCCTGATGAC

Alignment

ORF - retro_mdom_2021 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.12 %
• Parental protein coverage: 98.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGPRLLDWASSPPHLQFNKFVLTGYRPASSGSGCLRSLFYLHNELGNIYTHGLALLGFLVLLPLTMPWGQ
          SGPRLLDW...P.HLQFN.F.LTGYRPASS.SGC.RSLFYLHNELGNIY.H.LALL.FLV.LPLT.PW.Q
Retrocopy SGPRLLDWINTPSHLQFNPFILTGYRPASSVSGCVRSLFYLHNELGNIYIHVLALLTFLVMLPLTIPWDQ

Parental  LGGGGWLGGTHCVACLAPPAGSVLYHLFMCHRGGSPVYARLLALDMCGVCLVNTLGALPIIHCTLACRPW
          LG.G.WLG.TH..ACLAPPAGS.LYHLFMCHRGG..VY..LLALDMCGV.L.N.LGA.P.I.CTL.C.P.
Retrocopy LGWGHWLGCTHFLACLAPPAGSILYHLFMCHRGGNRVYSHLLALDMCGVWLANSLGAIPMIQCTLLCWPC

Parental  LRPAALVGYTLLSGLAGWRALTAPSTSARLRAFGWQAGARLLVFGARGMGLGAGAPGSLPCYLRMDALAL
          LR..ALV.Y..LS..AGW.ALTA.ST.ARL.AFGWQA.ARLLVFG.R..GLG.GAP.SL.CYLRMDALAL
Retrocopy LRLFALVMYAFLSVMAGWWALTALSTTARLQAFGWQAIARLLVFGIRWLGLGTGAPRSLLCYLRMDALAL

Parental  LGGLVNVARLPERWGPGRFDYWGNSHQIMHLLSVGSILQLHAGVVPDLLWAARH--ACPKD
          LGGLVNVARLPERWGPG.FDYW.NSHQIMH.LSV.SILQ.HAGV.PDL.WAA.H..ACP.D
Retrocopy LGGLVNVARLPERWGPGIFDYWCNSHQIMHFLSVISILQMHAGVIPDLVWAASHDYACPDD

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_2021 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2021 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001349	1 retrocopy	retro_meug_1124,
Monodelphis domestica	ENSMODG00000016528	1 retrocopy	retro_mdom_2021 ,
Sarcophilus harrisii	ENSSHAG00000017610	1 retrocopy	retro_shar_18,