RetrogeneDB ID: retro_meug_375

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold107138:1893..2681(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSMEUG00000014458
• Aliases: None
• Description: penta-EF-hand domain containing 1 [Source:HGNC Symbol;Acc:30009]

Sequence

>retro_meug_375
CCCAGCAGTTATTACCCAGGACATTCCCAGTATGAAGGGGGGCTACCCCTGGTGGGAGTTATGGAAGTCCAGCTCTTGGA
GGGTCCTACAGACCACCATCTGCTGCAGAAGCCTATGGACATCCCAGCCCTGGGGGGATCCCCTCATCAGCTCCTGGAGG
ACTCTATGGATGTTCTGCCCTGGGAGGTCCCAATGGCCAGCCTGCTACAAATCCCTATAACATCCCTCAAGGAGGACCTT
TTGGGCAAAGCCCATCAGCAGGCAGCATTCCTCCTGGTGTAGACCCCAAAGCTTACTCCTGGTTCCAGACAGTGGATTCA
GATCACAATGGCTACATCTCTGCGAAGGAACTCAAGCAGGTCTTGGTCAACTTCAATTGGTCTGCATTCAATGATAAAAC
CTGCCTCATGATGATAAACATGTTTGACAAGACCAAGACAGGTCAGATCAACTTCTTTGGCATTTCTGCCTTGTGGACCT
TTATCAAGCAGTGGAAGAACTTCTTCCAGCAATATGACTGGGACCACTCAGGCTGCATTAGCTACAATAAGTTGCAGCAA
GCTCTGTCTCAGATGGGCTACAACCTGAGCCCTCAGTTCACCCAGCTTCTGCTCTCCCGGTTATGCCCACATTCTGTCAA
CCCTGCCATGCAGCTGGATCACTTCATCCAGGTGTGCACCCAGTTGCAGGTGCAGACCGAGGCTTTCCGAGAGAAGGACA
CTAGCATGCACAGTAGTTTCTGGCTCAGCTTTGAGGAGGTTCTCATCATCATAACCTCACAGATGTTG

Alignment

ORF - retro_meug_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.92 %
• Parental protein coverage: 92.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGSYYSGHPQYGGGLP-PGGGYGGPAPGGPYRPPSGGGAYGHPSPGGHPSSAPGGPYGGSAPGGPYGQPA
          P.SYY.GH.QY.GGLP.PGG.YG.PA.GG.YRPPS...AYGHPSPGG.PSSAPGG.YG.SA.GGP.GQPA
Retrocopy PSSYYPGHSQYEGGLP<PGGSYGSPALGGSYRPPSAAEAYGHPSPGGIPSSAPGGLYGCSALGGPNGQPA

Parental  TNPYNTPQAGPYGQ----GSIPPGVDPEAYSWFQTVDSDHSGYISVKELKQALVNSNWSAFNDETCLMMI
          TNPYN.PQ.GP.GQ....GSIPPGVDP.AYSWFQTVDSDH.GYIS.KELKQ.LVN.NWSAFND.TCLMMI
Retrocopy TNPYNIPQGGPFGQSPSAGSIPPGVDPKAYSWFQTVDSDHNGYISAKELKQVLVNFNWSAFNDKTCLMMI

Parental  NMFDKTKTGRIDLFGFSALWTFIQQWKNLFQQYDRDHSGSISYNELQQALSQMGYNLSPQFTQLLLSRYC
          NMFDKTKTG.I..FG.SALWTFI.QWKN.FQQYD.DHSG.ISYN.LQQALSQMGYNLSPQFTQLLLSR.C
Retrocopy NMFDKTKTGQINFFGISALWTFIKQWKNFFQQYDWDHSGCISYNKLQQALSQMGYNLSPQFTQLLLSRLC

Parental  PRSANPAMQLDRFIQVCTQLQVLTEAFREKDTSMQGSVRLSFEEFLIMTASRML
          P.S.NPAMQLD.FIQVCTQLQV.TEAFREKDTSM..S..LSFEE.LI...S.ML
Retrocopy PHSVNPAMQLDHFIQVCTQLQVQTEAFREKDTSMHSSFWLSFEEVLIIITSQML

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_375 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_375 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375 ,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,