RetrogeneDB ID: retro_meug_1315

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold36611:16980..17425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EFHD1
• Ensembl ID: ENSMEUG00000008640
• Aliases: None
• Description: EF-hand domain family, member D1 [Source:HGNC Symbol;Acc:29556]

Sequence

>retro_meug_1315
CCCTGGCCTGCTAAGGTATTCAAACCCTACATCAAGATCCCAGAGTTCTGGCACATCAAGGACAGGGAGAGCCTCTTCCA
ACAGTATGACCATGGCAAAGGTGGCTACATCAACCTGATGGAACTGAAGCTGGTGATGGAGAAGCTGGGATCTCCCTAGA
CCCATCTGGGGCTTAAGAACATGAGCAAGGAGGTGGATGAAAATTTAGACAGATAGTAGAGCTTTTGAGTTTTTGCTGAT
TCCTGAGGGAACTGGAGGAGGACAGCAGCTAATGTCTCTGGCCAAGCTTTCAGAGGTCAATGTGGCCATCAAAGGAGTGA
AAGGGGCCAAGAACTTCTTTGAAGCCAAGGTCCATGCCCTGTCTCTGACCAGTAGATTTGAACCTGAGATCAAAGCAGAG
GAAATGTCCTGAAAACCAGAGAAAGAAGAGGAGAGGAAACACCAG

Alignment

ORF - retro_meug_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.84 %
• Parental protein coverage: 84.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRPTKVFKPYTEFPEFSRRQIKDMESLFRRYDSGKDGYIDLMELKLMMEKLGAPQTHLGLKNMIKEVDED
          P.P.KVFKPY...PEF....IKD.ESLF..YD.GK.GYI.LMELKL.MEKLG.P.THLGLKNM.KEVDE.
Retrocopy PWPAKVFKPYIKIPEFWH--IKDRESLFQQYDHGKGGYINLMELKLVMEKLGSP*THLGLKNMSKEVDEN

Parental  LD-SKLSFRELIFSRGALGVEEDSSLMALTKFPKTHVGPE-CTWVQNISEA-VHALSVTSRFEAEIKAEQ
          LD.....F..L....G..G......LM.L.K.....V.........N..EA.VHALS.TSRFE.EIKAE.
Retrocopy LD>DSRAFEFLLIPEGTGGGQQ---LMSLAKLSEVNVAIKGVKGAKNFFEAKVHALSLTSRFEPEIKAEE

Parental  MARKQEEEERRHRQ
          M..K.E.EE.R..Q
Retrocopy MS*KPEKEEERKHQ

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_1315 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1315 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
Choloepus hoffmanni	ENSCHOG00000003684	1 retrocopy	retro_chof_1298,
Equus caballus	ENSECAG00000024045	1 retrocopy	retro_ecab_85,
Macropus eugenii	ENSMEUG00000008640	1 retrocopy	retro_meug_1315 ,
Monodelphis domestica	ENSMODG00000010573	2 retrocopies	retro_mdom_1492, retro_mdom_211,