RetrogeneDB ID: retro_meug_544

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold13439:5245..6184(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSMEUG00000004960
• Aliases: None
• Description: CAP, adenylate cyclase-associated protein 1 (yeast) [Source:HGNC Symbol;Acc:20040]

Sequence

>retro_meug_544
TTTATAACAAACCCAGGTGCTCAAGGAATTCAAAGATGTGGATAAGAAGCATGTGGAGTGGGGTAAAAGCTACATGACTA
TCCGGACTGAGCTGCAGGCATACATTAAGGAGTACCATACCACTGTTCTAGCCTGGAGCAAAACGGGACCCACAGCAAAA
AACTGAGTTGCACATTGTCAGGCCCCTCAGCTGGCTCAACCCCTCCTCCCCCACCACCTAGACCTCCTCCTCCCCCCATC
CTCACGAGTTCTGGCTCTGATGAGTCTGCTTCTTGGTCGGCACTCTTTGCTCAGATTAATCAGGGAAAGGGAATCACACA
TGCTCTGAAATATGTATCAGATGACATGAAGACTCATAAGAATTCAGCCTTAAAGAGCCAGAGTGGACCCGTGCGCAGTG
GCCTCAAGCCTTTCACAGCTCCCAAGCCAGCTGGCGGAGCCACTCCCAAACTAGCTGCCAAGAAGGAACCGCCAGTGCTG
GAGCTGGAGGGCAAAAAGTGGAGAGTGGAAAACCAGGAGAATGTTTCCAACCTAGTGATAAATGACACAGAGCTGAAGCA
GGTGGCTTACATATACAAGTGTGTGAGTTCTACACTCCATATCAAGGGCAAAATCAGTTCCATCACATTAGATAACTGTA
AGAAGCTTGGCCTGCTGTTTGATGACGTCGTTGGGATTGTGGACATCATAAACAGCAAAGACATCAAAGTTCAGGTGATG
TGCAAAGTGCCAGCTATTTCCATCAAGAAGACAGATGGCTGCCATGTGTACCTGAGCAAGAATTCTCTGGACTATGAGAT
AGTCACTGCCAAGTCTTCTGAAATGAATGTCTTCATTCTCACAGAAAGTGGCGACTTTAAGGAATTCTCTGTCCCTGAGC
AGTTCAAGACACTGTGGAATGGGCAGAAGTTGGTTACCACAGTGACCAAAATTGCTGGA

Alignment

ORF - retro_meug_544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.08 %
• Parental protein coverage: 65.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FYTN-RVLKEFKDVDKKHVEWVKAYLTIWTELQAYIKEYHTTGLAWSKTGPTAK-ELSGTLSGPSAGSAP
          F.TN..VLKEFKDVDKKHVEW.K.Y.TI.TELQAYIKEYHTT.LAWSKTGPTAK..LS.TLSGPSAGS..
Retrocopy FITN>QVLKEFKDVDKKHVEWGKSYMTIRTELQAYIKEYHTTVLAWSKTGPTAK<KLSCTLSGPSAGSXX

Parental  PPPPPGPPPPPIPTSSGSDESASRSALFAQINQGEGITHALKHVSDDMKTHKNPALKSQSGPVRSGPKPF
          .............TSSGSDESAS.SALFAQINQG.GITHALK.VSDDMKTHKN.ALKSQSGPVRSG.KPF
Retrocopy XXXXXXXXXXXXXTSSGSDESASWSALFAQINQGKGITHALKYVSDDMKTHKNSALKSQSGPVRSGLKPF

Parental  TAPKPAGGATPKPAAKKEPPVLELEGKKW-VENQENVSNLVINDTELKQVAYVYKCVSSTLHIKGKINSI
          TAPKPAGGATPK.AAKKEPPVLELEGKKW.VENQENVSNLVINDTELKQVAY.YKCVSSTLHIKGKI.SI
Retrocopy TAPKPAGGATPKLAAKKEPPVLELEGKKWRVENQENVSNLVINDTELKQVAYIYKCVSSTLHIKGKISSI

Parental  TLDNCKKLGLVFDDVVGIVEIINSKDIKVQVMGKVPTISINKTDGCHVYLSKNSLDCEIVSAKSSEMNVL
          TLDNCKKLGL.FDDVVGIV.IINSKDIKVQVM.KVP.ISI.KTDGCHVYLSKNSLD.EIV.AKSSEMNV.
Retrocopy TLDNCKKLGLLFDDVVGIVDIINSKDIKVQVMCKVPAISIKKTDGCHVYLSKNSLDYEIVTAKSSEMNVF

Parental  IPTESGDFNEFPVPEQFKTLWNGQKLVTTVTEIAG
          I.TESGDF.EF.VPEQFKTLWNGQKLVTTVT.IAG
Retrocopy ILTESGDFKEFSVPEQFKTLWNGQKLVTTVTKIAG

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_544 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_544 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004417	1 retrocopy	retro_amel_1891,
Bos taurus	ENSBTAG00000013363	1 retrocopy	retro_btau_460,
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Equus caballus	ENSECAG00000024658	1 retrocopy	retro_ecab_119,
Homo sapiens	ENSG00000131236	2 retrocopies	retro_hsap_2666, retro_hsap_664,
Gorilla gorilla	ENSGGOG00000027527	2 retrocopies	retro_ggor_1860, retro_ggor_575,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544 ,
Myotis lucifugus	ENSMLUG00000011626	1 retrocopy	retro_mluc_847,
Mus musculus	ENSMUSG00000028656	1 retrocopy	retro_mmus_1265,
Nomascus leucogenys	ENSNLEG00000012077	2 retrocopies	retro_nleu_1600, retro_nleu_2221,
Otolemur garnettii	ENSOGAG00000005492	1 retrocopy	retro_ogar_299,
Pongo abelii	ENSPPYG00000001496	4 retrocopies	retro_pabe_2212, retro_pabe_2358, retro_pabe_2415, retro_pabe_584,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180,
Tursiops truncatus	ENSTTRG00000004358	1 retrocopy	retro_ttru_1689,