RetrogeneDB ID: retro_meug_842

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold206055:427..890(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMEUG00000012013
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VAPB
• Ensembl ID: ENSMEUG00000009788
• Aliases: None
• Description: VAMP (vesicle-associated membrane protein)-associated protein B and C [Source:HGNC Symbol;Acc:12649]

Sequence

>retro_meug_842
TATGATCCTAATGAAAAAGTAAACCCAAGTTTATGGTTCAATCTACATTTGCTCTGACTGACACCTCGGATATGGAAGCA
GTATGGAAGGAGGCAAAACCAGAAGATCTTATAGATTCAAAACTTAGGTGTGTGTGTGTGTTTGAATTGCAGGAAGAGAA
CGATAAACCACATGATGTAGAAATAAATAAAATTATGTCCCCAATGGCAACAAAGACAGAATCATCTGTTATATCTAAAT
CTATAGTTTTTCTTTGGATGATGCTGAAGCTAAGAAAATAATGGAAGAATGTAAAAGGCTACAAGTAGAAATTCAGAGGT
TACAGGAGGAAAACAAACAATTTAAGGAAGGAGATGGCTTTCACATGAGAAAGGCACTTCAGGGCAACATCCCAGCTTCC
ACTTCAGCCACCATTGAGAAGGAACAAGGGTTCAGTACCCAACTGCTGGCTTTGATTGTCTTG

Alignment

ORF - retro_meug_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.98 %
• Parental protein coverage: 72.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YDPNEK-SKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVF--ELPAENDKPHDVEINKIMSTT
          YDPNEK.SK.KFMVQS.FA.TDTSDMEAVWKEAKPEDL.DSKL......EL..ENDKPHDVEINKIMS..
Retrocopy YDPNEK<SKPKFMVQSTFALTDTSDMEAVWKEAKPEDLIDSKLXXXXXXELQEENDKPHDVEINKIMSPM

Parental  ATKTESSVMSKSI-SSSLDDTEAKKVMEECKRLQVEVQRLQEENKQFKEEDGLRMRKTLQSNSPASTSAT
          ATKTESSV.SKSI.S.SLDD.EAKK.MEECKRLQVE.QRLQEENKQFKE.DG..MRK.LQ.N.PASTSAT
Retrocopy ATKTESSVISKSI<SFSLDDAEAKKIMEECKRLQVEIQRLQEENKQFKEGDGFHMRKALQGNIPASTSAT

Parental  VVKEEGLSTRLLALVVL
          ..KE.G.ST.LLAL.VL
Retrocopy IEKEQGFSTQLLALIVL

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_842 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_842 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017424	1 retrocopy	retro_btau_1010,
Dasypus novemcinctus	ENSDNOG00000012711	1 retrocopy	retro_dnov_206,
Echinops telfairi	ENSETEG00000017229	1 retrocopy	retro_etel_1235,
Macropus eugenii	ENSMEUG00000009788	1 retrocopy	retro_meug_842 ,
Monodelphis domestica	ENSMODG00000016549	1 retrocopy	retro_mdom_919,
Nomascus leucogenys	ENSNLEG00000009351	1 retrocopy	retro_nleu_55,