RetrogeneDB ID: retro_sscr_538

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:15888921..15889465(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2B-LY6G5B
• Ensembl ID: ENSSSCG00000001414
• Aliases: CSNK2B, CK2N, CKII beta
• Description: Sus scrofa casein kinase 2, beta polypeptide (CSNK2B), mRNA. [Source:RefSeq mRNA;Acc:NM_001145377]

Sequence

>retro_sscr_538
TTTCGTGGGTTTGGTGGCAATGAATTCTTCTGTGAAATAGATGAAGACTACATCCAGGACAAATTTAACCTCAGTGACCT
CAATGAGCAGGTGCTTCACTATGGACAAGCTTTATATATGATCTCAATCTGAAGCCTGATGAAGAGTTGGACTACAACCC
CAGCCAGAGCGACCTAATTAAGCCAGCAGCTGAGATGCTGTATGGGTTGTCTCAGATCCCCTAAATCCTCACCAACCACG
GAAACACACAGGTTGGAAAACTATCAGCAGGAACACTTTGGCTATCACCTTACGTGCACTGTGAGAACAAGCCAAAACTT
CCCATTGGTGTTTCCGACGTGGCAGGTGGGGCCATGGTGAAGCCCTACTTCCTCAAATGCATTGATGTGTCCACACCCCA
AGGCTTCACTGAAACAGCGCCACATGGAAGGCCCTGACTTGGACACCAGTTCCCCCCATATGTTCTTCATGGCACACTCT
GAATGCCGATCTAAGTGTCCCATCAACCAGTTTATGGCCCAAACGCCATACTTGGAAGATCCAT

Alignment

ORF - retro_sscr_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.38 %
• Parental protein coverage: 84.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMI-LDLEPDEELEDNPNQSDLIEQAAEMLYG
          F.G..GNEFFCE.DEDYIQDKFNL..LNEQV.HY.QAL.MI.L.L.PDEEL..NP.QSDLI..AAEMLYG
Retrocopy FRGFGGNEFFCEIDEDYIQDKFNLSDLNEQVLHYGQALYMI<LNLKPDEELDYNPSQSDLIKPAAEMLYG

Parental  LIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMVKLYCPKCMDVYT-PKSS-
          L.....ILTN.G..Q...K...G.....P.V.CEN.P.LPIG.SD..G.AMVK.Y..KC.DV.T.PK.S.
Retrocopy LSQIP*ILTNHGNTQ-VGKLSAGTLWLSPYVHCENKPKLPIGVSDVAGGAMVKPYFLKCIDVST>PKASL

Parental  RHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFV-PRLYGFKIH
          ...H..G....T..PHM.FM.H.E.R.K.P.NQF..P.....KIH
Retrocopy KQRHMEGPDLDTSSPHMFFMAHSECRSKCPINQFM>PKRHTWKIH

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	106.18 RPM
SRP014902_testis	0.00 RPM	90.67 RPM
SRP018288_heart	0.00 RPM	51.73 RPM
SRP018288_kidney	0.00 RPM	75.65 RPM
SRP018288_liver	0.00 RPM	52.29 RPM
SRP018288_lung	0.00 RPM	111.09 RPM
SRP018856_adipose	0.00 RPM	60.21 RPM
SRP035408_brain	0.00 RPM	64.76 RPM
SRP035408_liver	0.00 RPM	29.68 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_538 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_538 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005751	1 retrocopy	retro_acar_107,
Bos taurus	ENSBTAG00000008837	1 retrocopy	retro_btau_885,
Callithrix jacchus	ENSCJAG00000002996	1 retrocopy	retro_cjac_2700,
Dasypus novemcinctus	ENSDNOG00000018728	1 retrocopy	retro_dnov_697,
Dipodomys ordii	ENSDORG00000014179	1 retrocopy	retro_dord_45,
Erinaceus europaeus	ENSEEUG00000006417	2 retrocopies	retro_eeur_331, retro_eeur_555,
Echinops telfairi	ENSETEG00000015168	3 retrocopies	retro_etel_225, retro_etel_271, retro_etel_769,
Felis catus	ENSFCAG00000007642	2 retrocopies	retro_fcat_1749, retro_fcat_206,
Macropus eugenii	ENSMEUG00000004095	10 retrocopies	retro_meug_1158, retro_meug_1316, retro_meug_1598, retro_meug_187, retro_meug_1939, retro_meug_40, retro_meug_525, retro_meug_528, retro_meug_751, retro_meug_752,
Monodelphis domestica	ENSMODG00000015287	4 retrocopies	retro_mdom_1433, retro_mdom_1558, retro_mdom_704, retro_mdom_936,
Mustela putorius furo	ENSMPUG00000011129	1 retrocopy	retro_mputfur_154,
Oryctolagus cuniculus	ENSOCUG00000023483	2 retrocopies	retro_ocun_1477, retro_ocun_362,
Ochotona princeps	ENSOPRG00000012138	1 retrocopy	retro_opri_970,
Sarcophilus harrisii	ENSSHAG00000001478	2 retrocopies	retro_shar_672, retro_shar_693,
Sus scrofa	ENSSSCG00000001414	1 retrocopy	retro_sscr_538 ,
Tursiops truncatus	ENSTTRG00000014103	2 retrocopies	retro_ttru_1595, retro_ttru_1740,