RetrogeneDB ID: retro_meug_2016

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold79821:5631..6244(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD1
• Ensembl ID: ENSMEUG00000010655
• Aliases: None
• Description: OCIA domain containing 1 [Source:HGNC Symbol;Acc:16074]

Sequence

>retro_meug_2016
AGAAGAGTCTTTGCTGAATGTAAGCCAGAGAGCTTCTGGTACAGGTCTGTTCCCTTTTTCGCAACAAGTATGTTTGTTAC
TCAGAGATTCATTGCTAAAGGAATTCTTTCTGGTCACCCTAAATATGATTCTGCCCCTAAACTTGTATTTCCTTATGTAA
CAGGATACTTTGATGGAAAAATTTCCTATATAACTATCTTCCTGAGAAGTTTAAACAGCTTGAAAATTCTCCTCTTGGAA
AGCTCTGCATCTGGGACAGGAACGTCGATTTGCATCACCTGGGTATTTTTCACACAAGCCAGGATCTGACTCAAAAATAT
CTGAGGATTCATCTTTGGAGCATCTCTTACATCTGAAAGGAGTGCTAAAGAAGGTCCCATTCCTCCTTCTGAACCAATCC
CCTTCATTGCTTCCATGAATGAATCAACTCCTCCTGGGATTACTGATTATAAAACACAAGGTTGTGATACAACTGTGGAA
GAAAGTCCTAAGAGAAAAGCTGCTAACATATGAAGAGTTAAAGAATGAAAACAGAGAAATATATAAAGTAACCTTGTCAC
AAAAAAGTGACACTACACTCAAATCTATGCAGGAAACAACACTAAAAACACAA

Alignment

ORF - retro_meug_2016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.37 %
• Parental protein coverage: 90.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRVFAECNRESFWYRXXXXXXXXXXXXXXXXXXXILSSHPKYDSVPKLVFACVMGYFAGKISYV-KTCQE
          RRVFAEC..ESFWYR...................ILS.HPKYDS.PKLVF..V.GYF.GKISY......E
Retrocopy RRVFAECKPESFWYRSVPFFATSMFVTQRFIAKGILSGHPKYDSAPKLVFPYVTGYFDGKISYI<NYLPE

Parental  KFKWLENSPLG-EALRLGQGCQ-ASPGYFSQKSGFESKITEHLS-FGTSPTSESRKK---LPPYEPIPFS
          KFK.LENSPLG..AL.LGQ....ASPGYFS.K.G..SKI.E..S.FG.S.TSE...K....PP.EPIPF.
Retrocopy KFKQLENSPLG<KALHLGQERRFASPGYFSHKPGSDSKISEDSS<FGASLTSERSAKEGPIPPSEPIPFI

Parental  ASMNESXXXXXXXXXXXXPDTTVEESPKR-KVVTYEELRNKNRETYEVTLSQKGDTPLRSVQERTPKKQ
          ASMNES.............DTTVEESPKR.K..TYEEL.N.NRE.Y.VTLSQK.DT.L.S.QE.T.K.Q
Retrocopy ASMNESTPPGITDYKTQGCDTTVEESPKR>KLLTYEELKNENREIYKVTLSQKSDTTLKSMQETTLKTQ

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_2016 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2016 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011863	1 retrocopy	retro_cpor_928,
Echinops telfairi	ENSETEG00000005961	1 retrocopy	retro_etel_1731,
Latimeria chalumnae	ENSLACG00000014002	1 retrocopy	retro_lcha_88,
Macropus eugenii	ENSMEUG00000010655	2 retrocopies	retro_meug_1692, retro_meug_2016 ,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103,
Sarcophilus harrisii	ENSSHAG00000018132	1 retrocopy	retro_shar_74,
Ictidomys tridecemlineatus	ENSSTOG00000014963	1 retrocopy	retro_itri_986,