RetrogeneDB ID: retro_meug_2015

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold7982:28930..29564(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUCKS1
• Ensembl ID: ENSMEUG00000007829
• Aliases: None
• Description: nuclear casein kinase and cyclin-dependent kinase substrate 1 [Source:HGNC Symbol;Acc:29923]

Sequence

>retro_meug_2015
CTGGTCAATTATTCACAGTTTCAGGAAACTGATGATGCAGATGAAGATCATGGAAGAGATTCAGCTCCTCCAGCTAAGAA
AATTCGATCATCGCCCAGAGAGGCTAAAAACAAGAGGCAATCTGGGAAAAATTCACAGGAAGATAGTGAAGACTCTGAAG
AAAAAGATATGAAGACCAGGAAGGATAGTGAAGATCAAAAACATCACAAAAATGTTCGCCAGCAGCGCCAGTATCATCCA
AAGCAGCTTCCAAGCAGAGAGATGCTCATGGAAGACATGGACAGTGAAGAAGAACCAGAATAGGAAGAAGTGGCACCATT
CCAGGAGAAAGAAGAAGACTTCCTAATGGAAATGATGATGATGATAGTGATTAAGGAAGTTCAAAAAAAGAAAAAAACCA
AAAGATCATGAAGAAATCCAAGTCTGAAAGGAAAGAAAAGAAAATGCCCAAACTAGGCTAAAGGCTACAGTGACACCAAG
TCCAGTGAAAGGCAAAGGAAAAGTGGGCTGTCCCATAGCATCAAAGGCATCAAAGGAAAAGACTCCTTCCCCTAAAGAAG
AGGATGAGGAGCCCCTAGAAAAGAAAAAGTCTGATGATGAATGGTCTGAAGATGAAGCCCAGTCTGGGGAAGAT

Alignment

ORF - retro_meug_2015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.71 %
• Parental protein coverage: 95.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVDYSQFQESDDADEDYGRDSAPPAKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKKDDSHSPEDS
          .V.YSQFQE.DDADED.GRDSAPPAKKIRSSPREAKNKR.SGKNSQEDSEDSEEKD.KT.KD.....ED.
Retrocopy LVNYSQFQETDDADEDHGRDSAPPAKKIRSSPREAKNKRQSGKNSQEDSEDSEEKDMKTRKDS----EDQ

Parental  EDEKDHKNVHQWYQAASKAASKQRLMEDVGSEEEKEEEKEAPFQRKDSGSDEDILM-NDDDDDSVYASSK
          ...K......Q.........S...LMED..SEEE.E.E..APFQ.K.....ED.LM...DDDDS...S..
Retrocopy KHHKNVRQQRQYH--PKQLPSREMLMEDMDSEEEPE*EEVAPFQEKE----EDFLM<GNDDDDSD*GSXX

Parental  KKNKMIMKKFKPERKENKMHKPRL-KVTVTPSP--VKDKGKLGNPTASKASKKKTPSPKEEDEEQELPPP
          ........K.K..........P.L.....T..P..VK.KGK.G.P.ASKASK.KTPSPKEEDEE....P.
Retrocopy XXXXXXIMK-KSKSERKEKKMPKL<RLKATVTPSPVKGKGKVGCPIASKASKEKTPSPKEEDEE----PL

Parental  KKKKSANPPPEKFGDGSED
          .KKKS.....E......ED
Retrocopy EKKKSDDEWSEDEAQSGED

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_2015 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2015 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015 , retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,