RetrogeneDB ID: retro_amel_339

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192390.1:2443275..2443947(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000014513
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUCKS1
• Ensembl ID: ENSAMEG00000012950
• Aliases: None
• Description: nuclear casein kinase and cyclin-dependent kinase substrate 1 [Source:HGNC Symbol;Acc:29923]

Sequence

>retro_amel_339
CAGGAATTTAACGATGCCAAGAAAATTATGGAAGAGATTGAGACCTTCCAGCTAAGAAAATTCAGTCATCTTCCGGAGAA
GCTAAAAATAAGAGGTGATCTGGAAAGAATTCACAGGAAGACAGTGAGGACTCAGAAGAAAAAGATGTGAAGACCAAGGA
TGATTCTCAGCAGAGGACAATGAAGATGAAAAAGAAGCCCATAAGAATGTGCACCAGCAAGGCCGGCAGCCTCTAAAGCA
GTTTCCAAACGAGAGAGAGGTATTCATGGAAGATGTGGGCAGTGGAGAAGAAAGAACAAGAAGAGGAGGATGAGGCACCA
TTCCAGGAGGAAGATTCTGGCAGTGATGATGATTTCCTAATAGAAGATGATGATGTCAATGACTATGGCAGCTCAAAAAA
GAAAAACAAAAAGATGGTTAAGAAGTCCAAACCTGAGAGAAAAGAAAATGCCCAAACCCAGGCTAAAGGCTGCAGTGATG
TCAAGCCCTGTGAAAGGCAAAGGGAAAAGTAGGTCACCCCACAGCCTCAGAGACATCAAAGGAAAAGACTCCTTCTCTCA
AAGAAGAAGAGGAGGAACCAGAAAGCCCCCAGAAAAGAAAACCTCTGCAAGCCCTCCATCTGACAAATCAGGGGATATAG
GGTCTGAAGATGAAACCCAGTCTGGGGAGGAT

Alignment

ORF - retro_amel_339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.55 %
• Parental protein coverage: 93.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QESDDA-DEDYGRDSGPPAKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKKDDSH-SAEDSEDEKE
          QE..DA..E.YGRD...PAKKI.SS..EAKNKR.SGKNSQEDSEDSEEKDVKT.KDDS...........E
Retrocopy QEFNDA<QENYGRD*DLPAKKIQSSSGEAKNKR*SGKNSQEDSEDSEEKDVKT-KDDSQ<AEDNEDEK-E

Parental  DHKNVRQQ-RQAASKAASK-QREMLMEDVGS-EDEQEEEE-EAPFQEKDSGSDEDFLMEDDDDSDYGSSK
          .HKNV.QQ.R.AASKA.SK..RE..MEDVGS.E....EEE.EAPFQE.DSGSD.DFL.EDDD..DYGS..
Retrocopy AHKNVHQQ<RPAASKAVSK>EREVFMEDVGS>EKKEQEEEDEAPFQEEDSGSDDDFLIEDDDVNDYGSXX

Parental  KKNKKMVKKSKPERKEKKM-PKPRLKATVTPSPVKGKGKVGRPTASKASKEKTPSPKEDDEEPESPPEKK
          .....MVKKSKPERKE....P.........P...KGK.....P......K.K.............PPEKK
Retrocopy XXXXXMVKKSKPERKENAQ>PRLKAAVMSSPVKGKGKSR--SPHSLRDIKGKDSFSQRRRGGTRKPPEKK

Parental  PSASPPPEKSGDEGSEDEAQSGED
          .SASPP..KSGD.GSEDE.QSGED
Retrocopy TSASPPSDKSGDIGSEDETQSGED

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_339 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_339 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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.

---

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,