RetrogeneDB ID: retro_sscr_377

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:92418413..92419038(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1B
• Ensembl ID: ENSSSCG00000008941
• Aliases: None
• Description: MOB kinase activator 1B [Source:HGNC Symbol;Acc:29801]

Sequence

>retro_sscr_377
GGTAGTCGCTCCTCTAAAACATTTAAACCAAAAAAGAACATTCCCGAGGATTCTCACCAATATGAGCTCTTACAGCATGC
AAAGGCCATACTTGGCAGTGGAAACCTGTAGATGGCTGTCATGCTTCCTGAGGGGGAAGAGCTAAATGAGTAGGTTGCAA
TGAACATGGGTTTCTTCAATCAGAACATGCTTTATGGAACAATCACAGATTTTTGCACAGAAGAAATTTATCCTGTGATG
TTAGCTGGCTCAAAGTATGAATATCATTGGGCAGATGGAACAAACATAAAGAAGCCTATTAAGGACTCTGCACCAAAGCA
TATTGATTACATCATGGTGTGGGTTCAGGACCAGTTGAATGATGAGACATTATTTCCATCAAAAATTGGTGTCCCATTCC
TAAAGAATCTCATGTCTGTGGCAAAAACTACTCAAAAGCCTCTTCTGGGTTTATGCTCACCTTTATCACCAGCATTTTGA
CCCTGCGATCTAGATTCAGGAGGAAGCACATCTCAATACATTGTTCAAGCACTTTATTTTTTTTGTCCAGGAATTCAACC
TTATTAACAGAAGAAAACTTGCACCATTCCAGGAACTGATTGAAAAACTCACTTCAAAGGACAGA

Alignment

ORF - retro_sscr_377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GSRSSKTFKPKKNIPEGSHQYELLKHAEATLGSGNLRMAVMLPEGEDLNEWVAVNTVDFFNQINMLYGTI
          GSRSSKTFKPKKNIPE.SHQYELL.HA.A.LGSGNL.MAVMLPEGE.LNE.VA.N...FFNQ.NMLYGTI
Retrocopy GSRSSKTFKPKKNIPEDSHQYELLQHAKAILGSGNL*MAVMLPEGEELNE*VAMN-MGFFNQ-NMLYGTI

Parental  TDFCTEESCPVMSAGPKYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDETLFPSKIGVPF-PKNF
          TDFCTEE..PVM.AG.KYEYHWADGTNIKKPIK.SAPK.IDY.M.WVQDQL.DETLFPSKIGVPF.PK..
Retrocopy TDFCTEEIYPVMLAGSKYEYHWADGTNIKKPIKDSAPKHIDYIMVWVQDQLNDETLFPSKIGVPF<PKES

Parental  MSVAKT-ILKRLFRVYAHIYHQHFDPVIQLQEEAHLNTSFKHFIFFVQEFNLIDRRELAPLQELIEKLTS
          ....K...LK.LF.VYAH.YHQHFDP.I..QEEAHLNT.FKHF...VQEFNLI.RR.LAP.QELIEKLTS
Retrocopy HVCGKN<LLKSLFWVYAHLYHQHFDPAI*IQEEAHLNTLFKHFXXXVQEFNLINRRKLAPFQELIEKLTS

Parental  KDR
          KDR
Retrocopy KDR

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	1.73 RPM
SRP014902_testis	0.00 RPM	5.52 RPM
SRP018288_heart	0.08 RPM	7.88 RPM
SRP018288_kidney	0.00 RPM	4.24 RPM
SRP018288_liver	0.00 RPM	2.72 RPM
SRP018288_lung	0.10 RPM	8.76 RPM
SRP018856_adipose	0.11 RPM	1.67 RPM
SRP035408_brain	0.03 RPM	0.48 RPM
SRP035408_liver	0.00 RPM	0.82 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_377 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_377 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012418	3 retrocopies	retro_chof_1124, retro_chof_1337, retro_chof_660,
Macropus eugenii	ENSMEUG00000014210	1 retrocopy	retro_meug_384,
Microcebus murinus	ENSMICG00000006469	2 retrocopies	retro_mmur_1622, retro_mmur_653,
Myotis lucifugus	ENSMLUG00000005838	1 retrocopy	retro_mluc_1067,
Ochotona princeps	ENSOPRG00000009133	1 retrocopy	retro_opri_386,
Sus scrofa	ENSSSCG00000008941	2 retrocopies	retro_sscr_377 , retro_sscr_586,
Vicugna pacos	ENSVPAG00000011892	1 retrocopy	retro_vpac_35,