RetrogeneDB ID: retro_meug_1890

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold69320:9420..9918(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSMEUG00000003940
• Aliases: None
• Description: NSFL1 (p97) cofactor (p47) [Source:HGNC Symbol;Acc:15912]

Sequence

>retro_meug_1890
TTTGCAGGAAGCAGATACCATCTTGGGGCAACCCCAGAGGTGGAGTCGAGCTACATAGCAGGTGAAAGATGACAATTTGT
GACCAAGATACACATACTGTATTGAAGATTTAAAAGAATGAATTTAGCCTGGACAATGGTGAGCAGAGAAGCTACCAAGA
TCACCTAACGTCCAGTTTCTGGAGTCTATCCACAGAGGTGAAGTACCTACAAAACTATGAAGGTTATCACATAGGGGACA
GATCAACTTGACCATGGAGGGCCATTGAGATAAGGACTTTGTAAAGCCCAAGGGAACCTTGAAATCATTCACTGTCAAGG
GTCAAAACCTGGGGAGTGCTACTCCCTCTCCTTAATTATTGAACATAAGTTCTCCAGCACAGAAGGCAAAAAATCAGCTA
AAAACAGTTCCTCCATAGCAACTGATGAGTCAGAGCCCTTTACCAAGATCCAAATCTGGCTCACTGATGGCAAGAGACTG
GTACAGAAATTTAATCAC

Alignment

ORF - retro_meug_1890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.65 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FAGGGYRLGAAPEEESAYVAGERRQF-SGQDVHIVLKLWKSGFSLDSGELRSYQD-PSNAQFLESIRRGE
          FAG..Y.LGA.PE.ES.Y.AGER.QF...QD.H.VLK..K..FSLD.GE.RSYQD...N.QFLESI.RGE
Retrocopy FAGSRYHLGATPEVESSYIAGER*QF<CDQDTHTVLKI*KNEFSLDNGEQRSYQD<SPNVQFLESIHRGE

Parental  VPTELRRLSRGGQVNLDMEDHRDEDFVKPKGTFKAFTGEGQKLGSTTPQ--VLNTSSPAQQAENE-AKAS
          VPT.L.RLS..GQ.NL.ME.H.D.DFVKPKGT.K.FT..GQ.LGS.TP....LN.SSPAQ.A.N..AK.S
Retrocopy VPTKL*RLSHRGQINLTMEGH*DKDFVKPKGTLKSFTVKGQNLGSATPSP*LLNISSPAQKAKNQ<AKNS

Parental  SSIAIDESEPTTNIQIRLADGGRLVQKFNH
          SSIA.DESEP.T.IQI.L.DG.RLVQKFNH
Retrocopy SSIATDESEPFTKIQIWLTDGKRLVQKFNH

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_1890 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1890 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890 , retro_meug_605,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,