RetrogeneDB ID: retro_sscr_804

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:71273312..71273747(+)
• Located in intron of: ENSSSCG00000023976

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSSSCG00000016079
• Aliases: MOBKL3, PREI3
• Description: MOB family member 4, phocein [Source:HGNC Symbol;Acc:17261]

Sequence

>retro_sscr_804
ATGGTCATGGCAGAGGGGATGATTGTGCTGAGGGGGAACAGGCCAGGCACCAAGGCTCAGGATTTCTCTAATTGGACTGA
TGAATCCTTTGATGAAATGGACAGTACCCTAGCTATTCAGCAGTATATTCAACAGAACATAAGAGCATATTGTTTCAATA
CTGACAACATTCCTGAACCACCTGAAAGCCAAGAATGAAGGTGTATGGAAGTATGAACATTTAAGAAAATTCTGTCTTGA
GCTAAATGGACTTGCTGTCAAATTCAGAGAGAATGCCATCTAGGTACATGTACTCCGATGATAGCAAGTGAACAATGGAT
TTTTCTTTGTACAGCTCATAAAACTCCAAAAGAGTGTCCTGACATAGACTATACTAGATATACACTTGATGGTGCTTCAT
GTCTTCTGAACAGCAATAAATATTTTCCCAGCAGG

Alignment

ORF - retro_sscr_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVMAEGTAVLRRNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQD-EGVW
          MVMAEG..VLR.NRPGTKAQDF.NW.DESFDEMDSTLA.QQYIQQNIRA.C.N.D.I.EPPE.Q..EGVW
Retrocopy MVMAEGMIVLRGNRPGTKAQDFSNWTDESFDEMDSTLAIQQYIQQNIRAYCFNTDNIPEPPESQE>EGVW

Parental  KYEHLRQFCLELNGLAVK-LQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNS
          KYEHLR.FCLELNGLAVK..Q.ECH..TCT.M.A.EQWIFLC.AHKTPKECP.IDYTR.TLDGA.CLLNS
Retrocopy KYEHLRKFCLELNGLAVK<IQRECHLGTCTPMIASEQWIFLCTAHKTPKECPDIDYTRYTLDGASCLLNS

Parental  NKYFPSR
          NKYFPSR
Retrocopy NKYFPSR

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	7.17 RPM
SRP014902_testis	0.00 RPM	6.08 RPM
SRP018288_heart	0.00 RPM	14.22 RPM
SRP018288_kidney	0.00 RPM	11.62 RPM
SRP018288_liver	0.00 RPM	4.16 RPM
SRP018288_lung	0.00 RPM	4.17 RPM
SRP018856_adipose	0.00 RPM	11.30 RPM
SRP035408_brain	0.00 RPM	4.80 RPM
SRP035408_liver	0.00 RPM	5.84 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_804 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_804 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_804 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000932	1 retrocopy	retro_etel_952,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Nomascus leucogenys	ENSNLEG00000006881	2 retrocopies	retro_nleu_287, retro_nleu_376,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Pan troglodytes	ENSPTRG00000012775	3 retrocopies	retro_ptro_1609, retro_ptro_626, retro_ptro_640,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Sus scrofa	ENSSSCG00000016079	2 retrocopies	retro_sscr_804 , retro_sscr_824,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,