RetrogeneDB ID: retro_sscr_1181

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:140488639..140489412(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAT
• Ensembl ID: ENSSSCG00000010734
• Aliases: None
• Description: ornithine aminotransferase [Source:HGNC Symbol;Acc:8091]

Sequence

>retro_sscr_1181
TCTACAGTGGCTTCTGTGAACCAAGGGCATTGTCACCCAAAGATTATGAATGCTCTGAAGAGTCGGTGGACAAATTGACC
CGAATGTCTAGGGCTTTCCACCATAACGTGCTTGAGAATGTGAAGAGTATGTTACTAAACTTTTCAACTACCACGAGGTC
CTTCCTATGAATACAGAGGTGGAGCTGGAGAGACTGCCTGCAAAATTGCTCGGAAATGGGGATATACCATGAAGGGTATT
CCAAAATGCAAAGCAAAGATCATTTTTGAAGCTGGAAACGTTTGCGGGAAAACATTCTTCCGCTATCTGCAGTTCCATAG
ACCCCACCACTCACGATGGTTTTGGACCATTTATGCCAGGTTTTGAAATCATTCCATATAACGATCTGCCTGCTCTAGAG
CATGTGCTGCAGGAGCCAAACGTTGCTGCGTTCATGGTAGAGGCAATTCAGGGTGAGGTGGGCATCGGTGTTCCAGATCC
AGGCTACCTCATGGGCTTGCATGAGCTCTGCACCCAGCACCAGGTTCTGTCTATTGCTGATCAAATACAGACAGGATTGG
CCAGAACTTGTCGATGTCTGGCTGTCGATCATGAAAATGTCAGGGCTGATATAGTCCTTCTAGGAAAGGCATTTCTGGTA
GTTTATACCCTGTCATCTCCGTGGTATTGTGTGATGATGATATAATGTTGACCATTAAGCCAGGGGAACATGGTCAATGT
ATGGTGGCAATCCACTGGGCTGCTGAGCGGCCATTGCAGCCCTTGAGGTTTTG

Alignment

ORF - retro_sscr_1181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.36 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SAYSAVNQGHCHPKIVNALKRQ-VDKLTLTSRAFYNDVLG-EYEEYITKLFNYHKVLPMNTGVE-AGETA
          S....VNQGHCHPKI.NALK...VDKLT..SRAF...VL..E.EEY.TKLFNYH.VLPMNT.VE.AGETA
Retrocopy STVASVNQGHCHPKIMNALKSR<VDKLTRMSRAFHHNVLE<ECEEYVTKLFNYHEVLPMNTEVE<AGETA

Parental  CKIARRWGYTVKGIPKYKAKIIFAAGNFWGRTL-SAISSSTDPTSYDGFGPFMPGFEIIPYSDLPALERA
          CKIAR.WGYT.KGIPK.KAKIIF.AGN..G.T..SAI.SS.DPT..DGFGPFMPGFEIIPY.DLPALE..
Retrocopy CKIARKWGYTMKGIPKCKAKIIFEAGNVCGKTF>SAICSSIDPTTHDGFGPFMPGFEIIPYNDLPALEHV

Parental  LQDPNVAAFMVEPIQGEAGVVVPDPGYLVGVRELCTQHQVLFIADEIQTGLARTGRWLAVDHENVRPDII
          LQ.PNVAAFMVE.IQGE.G..VPDPGYL.G..ELCTQHQVL.IAD.IQTGLART.R.LAVDHENVR.DI.
Retrocopy LQEPNVAAFMVEAIQGEVGIGVPDPGYLMGLHELCTQHQVLSIADQIQTGLARTCRCLAVDHENVRADIV

Parental  LLGKA-LSGGLYPV-SAVLCDDEIMLTIKPGEHG-STYGGNPLGCRVAIAALEVL
          LLGKA..SG.LYPV.S.VLCDD.IMLTIKPGEHG.S.YGGNPLGC..AIAALEVL
Retrocopy LLGKA<ISGSLYPVISVVLCDDDIMLTIKPGEHG<SMYGGNPLGC*AAIAALEVL

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	17.12 RPM
SRP014902_testis	0.00 RPM	119.52 RPM
SRP018288_heart	0.00 RPM	97.78 RPM
SRP018288_kidney	0.00 RPM	66.59 RPM
SRP018288_liver	0.00 RPM	77.72 RPM
SRP018288_lung	0.00 RPM	180.84 RPM
SRP018856_adipose	0.00 RPM	217.74 RPM
SRP035408_brain	0.00 RPM	119.74 RPM
SRP035408_liver	0.00 RPM	130.02 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1181 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176, retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989, retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181 ,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87,