RetrogeneDB ID: retro_amel_1711

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194054.1:290018..290496(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSAMEG00000000012
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1, cytosolic [Source:HGNC Symbol;Acc:18170]

Sequence

>retro_amel_1711
GAGAAATACGGCTGCACACACCCCCCTTCTGCGGGAGAACTTCTTCGTGATGAAAAGGAAGAAGCCAGATTCACAGGACG
GTGAAGTCTTAGAAAAGTACATTAAAGATGGAAAGGTTGTGCCAGTGGGATAACCATCAGTTTGTTAAAGGAGGAAAGGA
ATCAGATCCATGCGCAGAAGAAGAGATTCGTGATTGAGGGGTTTCCAAGAGATCAGAGACAACCTTCAAAGTTGGGGCAA
GACCATGGGTGGGAGGACAGACTGTAACCTTCCTTCTGTGGTTTGACTGTAATAATGGGATCTGTATTGAACCATGTCTT
GGGAGGAGAAAGAGGAGTGGTAGAAGTGATGACAACCGAGAGAGAGCTTGGAAAAGAGAATTCCGACCCACATTCAGTCA
ACAAAGCCAATTATTGACTTAAAAGAAGAAATGGGGGAAGTCAAGGAAATAGATGCCTCTAAGTCTGTTGATGAAGTT

Alignment

ORF - retro_amel_1711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.47 %
• Parental protein coverage: 93.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QKYGYTHL-SAGELLRDE-RKNPDSQYGELIEKYIKDGKIVPVE-ITISLLKREKDQTMAANAQMNKFLI
          .KYG.TH..SAGELLRDE.RK.PDSQ.GE..EKYIKDGK.VPV..ITISLLK.E..Q.....AQ...F.I
Retrocopy EKYGCTHPPSAGELLRDE>RKKPDSQDGEVLEKYIKDGKVVPVG<ITISLLKEERNQI---HAQKKRFVI

Parental  DGFLRN-KDNLQGWKKTMDGKAD-VSFVLFFDCNNEICIERCLERGK-SSGRSDDN-RESLEKRIQTYLQ
          .GF.R...DNLQ.W.KTM.G..D.V.F.L.FDCNN.ICIE.CL.R.K.S....D...RESLEKRI.T..Q
Retrocopy EGFPRD>RDNLQSWGKTMGGRTD>VTFLLWFDCNNGICIEPCLGRRKRSGRSDDNR<RESLEKRIPTHIQ

Parental  STKPIIDLYEEMGKVKKIDASKSVDEV
          STKPIIDL.EEMG.VK.IDASKSVDEV
Retrocopy STKPIIDLKEEMGEVKEIDASKSVDEV

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_1711 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1711 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.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711 ,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652, retro_cjac_2992,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369,
Sorex araneus	ENSSARG00000009745	2 retrocopies	retro_sara_199, retro_sara_294,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,
Tupaia belangeri	ENSTBEG00000017494	2 retrocopies	retro_tbel_3597, retro_tbel_691,
Tarsius syrichta	ENSTSYG00000007511	1 retrocopy	retro_tsyr_319,
Vicugna pacos	ENSVPAG00000004127	2 retrocopies	retro_vpac_345, retro_vpac_373,