RetrogeneDB ID: retro_meug_109

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_2769:32579..33603(-)
• Located in intron of: ENSMEUG00000002029

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBQLN4
• Ensembl ID: ENSMEUG00000016573
• Aliases: None
• Description: ubiquilin 4 [Source:HGNC Symbol;Acc:1237]

Sequence

>retro_meug_109
CAAGAGATGATGCGTAACCAGGACCGGGCCCCGAGCAACCTGGAGAGCATCCCTGGGGGATACAATGCCTTGTGCCGCAT
GTACACAGACATCAGGAGCCCATGTTCAGTGCTGCTTGGGAACAGTTCGGCAACAATCCCTTCTCCTCGTTGTCGGGGAA
TTCTGACAGCTCCTCCTCCCAACCTCTCCAGACTGAGAACCGGGAGCCCCTCCCTCACCCTTGGAGCCCCTCAGCCCCCA
CCTCCCAGGCCCCAGGGCCTGCTGGGGAGGGCACCAGAGGCTCAGGGACCAGCCAGGTGCACCCAACAGTCTCCAACCCC
TTTGGGATCAACGCAGCTAGCCTGGGGTCAGGGATGTTTAATAGCCCTGAGATGCAAGGTCTTCTCCAGCAAATTTCAGA
GAATCCCCAGTTAATGCAAAACATGATCTCTGCCCTGTACACTTGAAGTATGATGCAGACACTTGCCCAGAACCCGGACT
TTGCTGCTCAGATGATGGTGAATGTCCCATTGTTTGCGGGAAACCCCCAGCTGCAGGAGCAGCTCAGGCTCCAGCTCCCT
GTCTTTTTACAGCAGATGCAGAACCCAGACTCGCTGTCCATTCTCACCAATCCCCGGGCCATGCAGGCCCTGCTACAGAT
TCAACTGGGGCTACAGATGCTGCAGACGGAGGCCCCAGGGCTGGTGCCCAGCCTTGGCAACTTTGGGGCACCCCGGATCC
CACCTCCCCCTACAGGAGGTAGCAGTGGTCCAGAGCCCCCATCACTTCCCAATCCACGCCAGCTAGTGCCTCTTCAGGAG
GGGGCATCACCAGCCCCCAGCAGCAGCTGATGCAACAAATGATTCAACTTTTGGCTGGAGGAGGAAATTCCCAGGTGCAG
ACACCAGAAATTCGATTTCAGCAACAGCTGGAGCAGCTCAATGCCATGGGCTTCATCAACCGAGAGGCTAACGTGCAGGC
CCTGATTGCTACGGATGGGGATATTAATGTATCCATTGAGAGACTGCTGGGCTCTCAGCCCTCC

Alignment

ORF - retro_meug_109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.9 %
• Parental protein coverage: 57.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QEMMRNQDRALSNLESIPGGYNALRRMYTDI-QEPMFSAAREQFGNNPFSSLSGNSDSSSSQPLRTENRE
          QEMMRNQDRA.SNLESIPGGYNAL.RMYTDI.QEPMFSAA.EQFGNNPFSSLSGNSDSSSSQPL.TENRE
Retrocopy QEMMRNQDRAPSNLESIPGGYNALCRMYTDI<QEPMFSAAWEQFGNNPFSSLSGNSDSSSSQPLQTENRE

Parental  PLPNPWSPSAPTSQAPGPAGEGTGGSGTSQVHPTVSNPFGINAASLGSGMFNSPEMQGLLQQISENPQLM
          PLP.PWSPSAPTSQAPGPAGEGT.GSGTSQVHPTVSNPFGINAASLGSGMFNSPEMQGLLQQISENPQLM
Retrocopy PLPHPWSPSAPTSQAPGPAGEGTRGSGTSQVHPTVSNPFGINAASLGSGMFNSPEMQGLLQQISENPQLM

Parental  QNMISAPYMRSMMQTLAQNPDFAAQMMVNVPLFAGNPQLQEQLRLQLPVFLQQMQNPDSLSILTNPRAMQ
          QNMISA.Y..SMMQTLAQNPDFAAQMMVNVPLFAGNPQLQEQLRLQLPVFLQQMQNPDSLSILTNPRAMQ
Retrocopy QNMISALYT*SMMQTLAQNPDFAAQMMVNVPLFAGNPQLQEQLRLQLPVFLQQMQNPDSLSILTNPRAMQ

Parental  ALLQIQQGLQTLQTEAPGLVPSLGNFGAPRIPPPPTGG-AGSEP-PITSQSTPASASSGGGTTSPQQQLM
          ALLQIQ.GLQ.LQTEAPGLVPSLGNFGAPRIPPPPTGG..G.EP.PITSQSTPASASSGGG.TSPQQQLM
Retrocopy ALLQIQLGLQMLQTEAPGLVPSLGNFGAPRIPPPPTGGSSGPEP<PITSQSTPASASSGGGITSPQQQLM

Parental  QQMIQLLAGGGNSQVQTPEIRFQQQLEQLNAMGFINREANLQALIATGGDINAAIERLLGSQPS
          QQMIQLLAGGGNSQVQTPEIRFQQQLEQLNAMGFINREAN.QALIAT.GDIN..IERLLGSQPS
Retrocopy QQMIQLLAGGGNSQVQTPEIRFQQQLEQLNAMGFINREANVQALIATDGDINVSIERLLGSQPS

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_109 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_109 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160803	1 retrocopy	retro_hsap_2859,
Gorilla gorilla	ENSGGOG00000008916	1 retrocopy	retro_ggor_26,
Macropus eugenii	ENSMEUG00000016573	1 retrocopy	retro_meug_109 ,
Microcebus murinus	ENSMICG00000002222	1 retrocopy	retro_mmur_1146,
Macaca mulatta	ENSMMUG00000009983	1 retrocopy	retro_mmul_905,
Monodelphis domestica	ENSMODG00000016961	1 retrocopy	retro_mdom_530,
Pan troglodytes	ENSPTRG00000001444	1 retrocopy	retro_ptro_1934,