RetrogeneDB ID: retro_meug_1104

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold29076:1189..2164(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3D
• Ensembl ID: ENSMEUG00000004561
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit D [Source:HGNC Symbol;Acc:3278]

Sequence

>retro_meug_1104
GCAAAATTCATGACTCCTGTGATCCAGGACAACCCCTAAGGCTGGGGTCCCTGTGCAGTCCCCAAACAATTTCGGGACAT
GTCCTATCAGCCCTTCAGTAAAGGAGATCGGCTGGGAAGTGTTGCAGACTGAACAGGGGTCACCTACCAGGATAAGAGGT
ACACGAATAAGTATTCCTCCCAGTTTAGGAGTGGAAGTCAATACGCTTATTTCCATGAGAAGGATAAGACCAGCTTCCAA
CTCGTAGACACTGCCCAGACCCAGAAGACGGCTTACCAAAGGAATAGGATGAGATTTGTCCAGCAGAATCTTCAGAGGGA
CAAGGACCGTCGGAACATGTTGCAGTTCAGCCTGCAGACCTTGCCCAAGAGCGCCAAACAGAGAGAGACCGCATACGTGT
GCAAAAAAAGTTTCAGAAGCAGTTTGGAGTAAGGCAGAAATGGGACCCCAAATCCCAGAAGCCCCGGGATTCTTCCGTTG
AGGTGAGGAGTGACTGGGAGGTGAAAGAAGAAATGGATTTTCCTCAGTTAAGGAAGATGCGTTACTTGGAGGTGTCAGAG
CCGCAGGACATCGAGTGTTGTGGCGCCCTAGGACATTAAGACAAAGCCTTTGACCAGATCACCACGAGGAATGAGAAGCC
TCTGCGTAGCATCAAGCCCATTTTCCACACCGTCACCACAACAGATGACCCCGTCATCCGCAAGCTGGCAAAGACTCAGG
GCAACGTGTTCGCCATGGATGCCATCCTAGTCATGCTGATGAGCTGCACACTCTCCGTCTATTCCTAGGATATTGTCGTC
CAGAAGGTTGGGTCCAAGCTCTTCTTTGACAAAAGGGACAACTCGGACTTTGACCTCCTGACTGTGAGCGAAACTGCCAA
CAAACCCCCTCAGATGAAGGCAACTCCTTCGACTCACCCTGGAACCCTTCCAGGATGCAACCTACATCAATCACAATTTC
TCCCAGCAGTGCCTG

Alignment

ORF - retro_meug_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.06 %
• Parental protein coverage: 60.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKFMTPVIQDNPSGWGPCAVPEQFRDMPYQPFSKGDRLGKVADWTGATYQDKRYTNKYSSQFGGGSQYAY
          AKFMTPVIQDNP.GWGPCAVP.QFRDM.YQPFSKGDRLG.VAD.TG.TYQDKRYTNKYSSQF..GSQYAY
Retrocopy AKFMTPVIQDNP*GWGPCAVPKQFRDMSYQPFSKGDRLGSVAD*TGVTYQDKRYTNKYSSQFRSGSQYAY

Parental  FHEEDETSFQLVDTARTQKTAYQRNRMRFAQRNLRRDKDRRNMLQFSLQTLPKSAKQKERDRIRLQKKF-
          FHE.D.TSFQLVDTA.TQKTAYQRNRMRF.Q.NL.RDKDRRNMLQFSLQTLPKSAKQ.E.......K.F.
Retrocopy FHEKDKTSFQLVDTAQTQKTAYQRNRMRFVQQNLQRDKDRRNMLQFSLQTLPKSAKQRETAYV-CKKSF<

Parental  QKQFGVRQKWDQKSQKPRDSSVEVRSDWEVKEEMDFPQLMKMRYLEVSEPQDIECCGALEYYDKAFDRIT
          QKQFGVRQKWD.KSQKPRDSSVEVRSDWEVKEEMDFPQL.KMRYLEVSEPQDIECCGAL...DKAFD.IT
Retrocopy QKQFGVRQKWDPKSQKPRDSSVEVRSDWEVKEEMDFPQLRKMRYLEVSEPQDIECCGALGH*DKAFDQIT

Parental  TRNEKPLRSIKRIFHTVTTTDDPVIRKLAKTQGNVFATDAILATLMSCTRSVYSWDIVVQRVGSKLFFDK
          TRNEKPLRSIK.IFHTVTTTDDPVIRKLAKTQGNVFA.DAIL..LMSCT.SVYS.DIVVQ.VGSKLFFDK
Retrocopy TRNEKPLRSIKPIFHTVTTTDDPVIRKLAKTQGNVFAMDAILVMLMSCTLSVYS*DIVVQKVGSKLFFDK

Parental  RDNSDFDLLTVSETANEPPQ-DEGNSFNSPRNLA-MEATYINHNFSQQCL
          RDNSDFDLLTVSETAN.PPQ.DEGNSF.SP.N.....ATYINHNFSQQCL
Retrocopy RDNSDFDLLTVSETANKPPQ<DEGNSFDSPWNPS<QDATYINHNFSQQCL

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_1104 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1104 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004561	2 retrocopies	retro_meug_1104 , retro_meug_1150,
Otolemur garnettii	ENSOGAG00000002978	2 retrocopies	retro_ogar_779, retro_ogar_991,