RetrogeneDB ID: retro_sscr_454

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:146130749..146131078(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CMPK1
• Ensembl ID: ENSSSCG00000003885
• Aliases: None
• Description: UMP-CMP kinase [Source:UniProtKB/Swiss-Prot;Acc:Q29561]

Sequence

>retro_sscr_454
AAGAATAAATTCCTAATTGATGGGTTTCCAAGAAATCAAGACAACCTTCAAGGCTGGAACAAGATCATGGATGAGAAGGC
TAATGTATCTTTCTTTCTGTTTTTTGACTGTAATAATGAGATCTGTATTGACCCATGTCTTGAGAGGGGAAAGAGTAGCA
GTGGGAGTGACGACAACAAAGAGAGCTTGGAAAAGAGAATTCAAACCTATCTTCAGTCAACAAAGCCAATTACTGACTTC
TATGAAGACATGGGGGAAGTCAAGAAAATGGGTGCTTCTCAATCTGTTGAAGTTTTGATGAAGTTGTGAAGATTTTTGAC
AAAGAAGGC

Alignment

ORF - retro_sscr_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.93 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNKFLIDGFPRNQDNLQGWNKTMDGKADVSFVLFFDCNNEICIERCLERGKSSGRSDDNRESLEKRIQTY
          KNKFLIDGFPRNQDNLQGWNK.MD.KA.VSF.LFFDCNNEICI..CLERGKSS..SDDN.ESLEKRIQTY
Retrocopy KNKFLIDGFPRNQDNLQGWNKIMDEKANVSFFLFFDCNNEICIDPCLERGKSSSGSDDNKESLEKRIQTY

Parental  LQSTKPIIDLYEEMGKVKKIDASKSVDEV-FDEVVKIFDKEG
          LQSTKPI.D.YE.MG.VKK..AS.SV.EV.FDEVVKIFDKEG
Retrocopy LQSTKPITDFYEDMGEVKKMGASQSV-EV<FDEVVKIFDKEG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	22.70 RPM
SRP014902_testis	0.00 RPM	13.15 RPM
SRP018288_heart	0.00 RPM	7.88 RPM
SRP018288_kidney	0.00 RPM	24.43 RPM
SRP018288_liver	0.00 RPM	19.67 RPM
SRP018288_lung	0.00 RPM	22.30 RPM
SRP018856_adipose	0.00 RPM	8.03 RPM
SRP035408_brain	0.00 RPM	4.10 RPM
SRP035408_liver	0.00 RPM	10.69 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_454 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_454 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000012	2 retrocopies	retro_amel_1074, retro_amel_1711,
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Callithrix jacchus	ENSCJAG00000021250	2 retrocopies	retro_cjac_2652, retro_cjac_2992,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417, retro_cpor_799,
Felis catus	ENSFCAG00000025426	1 retrocopy	retro_fcat_1259,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576,
Otolemur garnettii	ENSOGAG00000026904	2 retrocopies	retro_ogar_1589, retro_ogar_3204,
Pongo abelii	ENSPPYG00000001380	1 retrocopy	retro_pabe_1369,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940,
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,