RetrogeneDB ID: retro_sscr_560

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:262440..263014(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000024717
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1A1
• Ensembl ID: ENSSSCG00000014435
• Aliases: None
• Description: Casein kinase I isoform alpha [Source:UniProtKB/Swiss-Prot;Acc:O19175]

Sequence

>retro_sscr_560
AATTTTATACATAGGGACATTAAACCTGATAACTTCCTAATGGGTGTTGGGCTTCACTGTAATAAGTTATTCCTTATTGA
TTTTGGTTTGGCCAAAAAGTACAGAGACAACAGGACAAGGCAACACATACCATACACAGAAGACAAAAATCTCACTGGCA
CTGCCCAACATGCTAGCATCAATGCACATCTTGCTACTGAACAGAGTCACCGAGATGACATGGAACCATTGGGATGTTTC
GATGTATTTTCACGGAACCAGTCTGCCATTGCAAGGACTAAAGGCTGCGACAAAGAAGCAAAAATATGAAAAAATTAGCA
AAATGAAGATGTCCACATCTGTTGAGGTTTTATGTAAGGGGTTTCCTGCAGAATTTGCCATGTACTTTTGTGGTGGACTG
CGCTTTGAGGAAGCCCCAGATTACATGTACCTGAGGCAGCTCTTCCGCATTCTTGTCAGGACCCTGAACCACCAATGTGA
CTACACATTTGATTGGGCAATGTTAAAGCAGAAAGCAGCACAGCAGACAGCCTCTTCAAGTGCGCAGGGTCAGCAGGCCC
AAACCCCCACAGGT

Alignment

ORF - retro_sscr_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 57.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NFIHRDIKPDNFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSR
          NFIHRDIKPDNFLMG.G.HCNKLFLIDFGLAKKYRDNRTRQHIPY.EDKNLTGTA..ASINAHL..EQS.
Retrocopy NFIHRDIKPDNFLMGVGLHCNKLFLIDFGLAKKYRDNRTRQHIPYTEDKNLTGTAQHASINAHLATEQSH

Parental  RDDMESLGYVLMYFNRTSLPWQGLKAATKKQK-YEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFE
          RDDME.LG.....F.R........K...K..K.YEKIS..KMST.VEVLCKGFPAEFAMY...C.GLRFE
Retrocopy RDDMEPLG-CFDVFSRNQSAIARTKGCDKEAK>YEKISKMKMSTSVEVLCKGFPAEFAMY--FCGGLRFE

Parental  EAPDYMYLRQLFRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTG
          EAPDYMYLRQLFRIL.RTLNHQ.DYTFDW.MLKQKAAQQ.ASSS.QGQQAQTPTG
Retrocopy EAPDYMYLRQLFRILVRTLNHQCDYTFDWAMLKQKAAQQTASSSAQGQQAQTPTG

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	0.27 RPM	98.88 RPM
SRP014902_testis	0.28 RPM	96.47 RPM
SRP018288_heart	1.00 RPM	91.26 RPM
SRP018288_kidney	1.48 RPM	147.17 RPM
SRP018288_liver	0.80 RPM	73.08 RPM
SRP018288_lung	0.41 RPM	129.73 RPM
SRP018856_adipose	0.38 RPM	137.48 RPM
SRP035408_brain	1.62 RPM	33.41 RPM
SRP035408_liver	2.26 RPM	45.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_560 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Otolemur garnettii	ENSOGAG00000003253	2 retrocopies	retro_ogar_1195, retro_ogar_825,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560 ,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,