RetrogeneDB ID: retro_sscr_119

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:99745076..99745819(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSSSCG00000007278
• Aliases: None
• Description: Sus scrofa adenosylhomocysteinase (AHCY), mRNA. [Source:RefSeq mRNA;Acc:NM_001011727]

Sequence

>retro_sscr_119
ACTGTCACCAAGAGCAAGTTTGATAACCTCTATGGCTACCTGGAGTCCTTTAAACATGGCATCAAGCGGGCCATAGCTGT
GATGATTGCGGGAAAGGTGGCGGTGTAGCAGGCTATGGTGATGTAGGCAAGAGTTGTGCCCATGCCCAGAGGGATTTCAG
GGTTTGCACCATCTTAATGAAGACTGACCCCATCAACACACTTCAGGATGCCATGGAGGGCTATGAGGTGACTACCATGG
ATGAAGCCTGTCAAGAGGGCAACATGTTTGTCACCTTAGCTAATGGGTGTATTGACATCATCCTTGGTGGGACTTGCAAC
AGGTGAAAGATGCCACTGTGTGTAACAGTGGACACTCTGATGTGGAGATGGATGTCAATTGGCTGAACAAGAACACTGTG
GAGAAGGTGAACATCAAGCCCTACGTGGACCGCTACTTGTTGAAGAATGGGTACCACATCATCCTGCTTGCCAAGGGCTA
CTGGTCTACCTGGTTTGTGCCATGGACAACCCCAGCTTCGTGATGAGCAATTCCTTTACCAAGCAGATGCTGGCCAGATT
GAGCCGTGAATCCACCCAGACAGGTGCCCCAGCTGAACCCTTTTGGTCAAGAAACTGGAGGAAGCAGTGGCTAAAACCCA
CCAGGGCAAGCTGAATGTGAAACTGACCAAGTAAACTAAGAAGTAGGCTTAGTACCTGGGCATGTCCTGTGAGGGCCCCT
TCAAGCCTGATCATGACCACTAT

Alignment

ORF - retro_sscr_119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 59.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAV-VAGYGDVGKGCAQALRGFGARVIITEIDPINALQ
          .VTKSKFDNLYG..ES...GIKRA..VMIAGKVAV.VAGYGDVGK.CA.A.R.F....I....DPIN.LQ
Retrocopy TVTKSKFDNLYGYLESFKHGIKRAIAVMIAGKVAV<VAGYGDVGKSCAHAQRDFRVCTILMKTDPINTLQ

Parental  AAMEGYEVTTMDEACQEGNIFVT-TTGCIDIILGR-HFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKV
          .AMEGYEVTTMDEACQEGN.FVT...GCIDIILG.....Q.K.DA.VCN.GH.DVE.DV.WLN.N.VEKV
Retrocopy DAMEGYEVTTMDEACQEGNMFVTLANGCIDIILGG<DLQQVK-DATVCNSGHSDVEMDVNWLNKNTVEKV

Parental  NIKPQVDRYLLKNGHRIILLA-EGRLVNLGCAMGHPSFVMSNSFTNQVLA-QIELWTHPDKYPVGVHFLP
          NIKP.VDRYLLKNG..IILLA..G.LV.L.CAM..PSFVMSNSFT.Q.LA.QIE...HPD..P.....L.
Retrocopy NIKPYVDRYLLKNGYHIILLA<QGLLVYLVCAMDNPSFVMSNSFTKQMLA<QIEP*IHPDRCP-S*TLLV

Parental  KKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSREGPFKPDHYRY
          KKL.EAVA..H.GKLNVKLTK.T.K.A.YLGMS.EGPFKPDH..Y
Retrocopy KKLEEAVAKTHQGKLNVKLTK*TKK*A*YLGMSCEGPFKPDHDHY

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	22.43 RPM
SRP014902_testis	0.00 RPM	107.07 RPM
SRP018288_heart	0.00 RPM	34.89 RPM
SRP018288_kidney	0.00 RPM	147.46 RPM
SRP018288_liver	0.00 RPM	278.24 RPM
SRP018288_lung	0.00 RPM	45.92 RPM
SRP018856_adipose	0.00 RPM	37.99 RPM
SRP035408_brain	0.00 RPM	55.17 RPM
SRP035408_liver	0.00 RPM	220.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_119 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_119 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552,
Callithrix jacchus	ENSCJAG00000018303	7 retrocopies	retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Homo sapiens	ENSG00000101444	6 retrocopies	retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Otolemur garnettii	ENSOGAG00000016787	3 retrocopies	retro_ogar_3223, retro_ogar_3401, retro_ogar_3402,
Pongo abelii	ENSPPYG00000010935	9 retrocopies	retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes	ENSPTRG00000013414	7 retrocopies	retro_ptro_1015, retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119 ,
Tarsius syrichta	ENSTSYG00000007163	3 retrocopies	retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus	ENSTTRG00000003632	1 retrocopy	retro_ttru_1666,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,