RetrogeneDB ID: retro_meug_1994

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold77538:7569..7917(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDC4
• Ensembl ID: ENSMEUG00000000817
• Aliases: None
• Description: syndecan 4 [Source:HGNC Symbol;Acc:10661]

Sequence

>retro_meug_1994
ATAGAAGTGATGGACCCCTGGACCTCTACAAAGCACACTACTTCTCTTGAGCCTGCCAGATGATGAGGATGTGGGAGAGG
CCCTACTGGAACAAGAGCGTGATGACTTTGCACTGTCAGGCTCAGGAGACACAGGTGATAGCAAGTCATCTGAGACATTC
CTTAACACAGTTAAGCCATCGGTGCCCCTGGATAATTACATTCTTGAGCAGAGGGAACGTTCAAGCCAGGGTATAAGAAC
TCTGAAGAGCTGGAGGAGAATGGAATCTTGTCCAAGAAGAGATTTTCCTTTGAGGAAGAAAATATAAACAAAAAAGTGTC
AATGTGTGGCACTTCCTTCTCATCTTTG

Alignment

ORF - retro_meug_1994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.83 %
• Parental protein coverage: 65.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IEVLDS-LDLYEAPNFSGA-LPDDE--GVVVLEQGPDDFELSGSGDTXXXXXXXXXXXXXXXXMSLDNHI
          IEV.D..LDLY.A..FS.A.LPDDE..G...LEQ..DDF.LSGSGDT..................LDN.I
Retrocopy IEVMDP<LDLYKAHYFS*A<LPDDEDVGEALLEQERDDFALSGSGDTGDSKSSETFLNTVKPSVPLDNYI

Parental  VEQREPSNQDP-KDSEEPEENEILSKKSFSFEEEKINNKVSMSSTAQGSI
          .EQRE.S.Q...K.SEE.EEN.ILSKK.FSFEEE.IN.KVSM..T...S.
Retrocopy LEQRERSSQGI<KNSEELEENGILSKKRFSFEEENINKKVSMCGTSFSSL

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_1994 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1994 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000124145	1 retrocopy	retro_hsap_2579,
Gorilla gorilla	ENSGGOG00000004153	1 retrocopy	retro_ggor_1614,
Macropus eugenii	ENSMEUG00000000817	1 retrocopy	retro_meug_1994 ,
Nomascus leucogenys	ENSNLEG00000006698	1 retrocopy	retro_nleu_759,