RetrogeneDB ID: retro_meug_1494

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold42618:1124..1816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSMEUG00000006596
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_meug_1494
CTCAAGCTGGTGTTGCTGGAGCTCAACTTCCTGCCTACCACGGGTACAAAACTGACTAAACAACAGCTCATTCTGGCCCA
TGACATCTTGGAGATTGGTGCCCAATGCAACATTTTGCAGAAAGACATACCTTCCTTGGAGTGATGCATGGCTCAGCTTA
AATGCTATTATTTTGACTACATGAATCAGCTCCCCAAGTCAGCCTACATACATCAGCATCTGGGCCTCAGTCTGCTCTTC
CTGCTGTCCCAGAACCGAGTGGCCAAGTTCCACACTGAGCTGGAGCGGCTCCCTGCTAAGGCCATCCAGACCAATGTCTA
CATCAGGCACCCTGTGTCCTTAGAGCAGTACCTAATGGAAGGGAGTTACAATAAGGTGTTCCTGGCCAAGGGAAATATCC
CTGCTGAGAGCTACATGTTCTTCATTGACATTTTGCTGGACACGATAAAGGGTGAGATTGCTGGCTGCATTGAGAAGGCC
TATGAAAAGATTTTGTTTGCTGAAGCCATGAGAATTCTTTTCTTCACCACTCCCAAGATGACTGAGTATGCCAAGAAGAG
ATGATGGGTCCTGTGCCCCAGCAATACTACAGCTTCAAGTGCCAGCAGCAGAAGCCTGAGGATACCACCATCCCCTCCAC
AGAGCTGGCAAAGTGAGTCATTGAATATGAGAGGCAGCTGGAGATGATTGTT

Alignment

ORF - retro_meug_1494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.84 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKLVLLELNFLPTTGTKLTKQQLILARDILEIGAQWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYM
          LKLVLLELNFLPTTGTKLTKQQLILA.DILEIGAQ..IL.KDIPS.E..MAQLKCYYFDY..QLP.SAY.
Retrocopy LKLVLLELNFLPTTGTKLTKQQLILAHDILEIGAQCNILQKDIPSLE*CMAQLKCYYFDYMNQLPKSAYI

Parental  HQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTF
          HQ.LGL.LLFLLSQNRVA.FHTELERLPAK.IQTNVYI.HPVSLEQYLMEGSYNKVFLAKGNIPAESY.F
Retrocopy HQHLGLSLLFLLSQNRVAKFHTELERLPAKAIQTNVYIRHPVSLEQYLMEGSYNKVFLAKGNIPAESYMF

Parental  FIDILLDTIRDEIAGCIEKAYEKILFAEATRILFFTTPKKMTEYAKKRGWVLGPSN-YYSFKCQQQKPED
          FIDILLDTI..EIAGCIEKAYEKILFAEA.RILFFTTP.KMTEYAKKR.WVL.PSN.YYSFKCQQQKPED
Retrocopy FIDILLDTIKGEIAGCIEKAYEKILFAEAMRILFFTTP-KMTEYAKKR*WVLCPSN<YYSFKCQQQKPED

Parental  TTIPSTELAKQVIEYARQLEMIV
          TTIPSTELAK.VIEY.RQLEMIV
Retrocopy TTIPSTELAK*VIEYERQLEMIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1494 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1494 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006596	2 retrocopies	retro_meug_1494 , retro_meug_173,
Macaca mulatta	ENSMMUG00000031219	1 retrocopy	retro_mmul_534,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,