RetrogeneDB ID: retro_sscr_1019

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:10014644..10015147(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD4
• Ensembl ID: ENSSSCG00000015776
• Aliases: None
• Description: RWD domain containing 4 [Source:HGNC Symbol;Acc:23750]

Sequence

>retro_sscr_1019
CTGGGTGCCAAGAAGGACAAGGAGGTGGGACGGGAAGTGTGGCACTGCATTGAAGAAGGAGATGGAACGTTTCTGAGAGT
TAAGTCCGGTTTCATTTCTATAGGGGTAGGTGAAAGTGGTGACCCCAAAGCTTTCTTCCTGGAGCTCTCCGGGACAGACA
CATATCCCCAACCACTTCCAATCTCATCTATGAATGCATCTTTTAACACCGTATTATCGGCTGTCAGCAGAGCACAGAAG
CCAAGTTATAGGAAGCAGTGGAAGTTAATCTCAGGCCCGCCATGACCTACACGTTGTCTGAATACACCAAGGACAAGAAG
AGCAGTTCATGGAGAATTACCATCCTGTTAATTCTATGTCATCCATAAGCAAGATCATCTCAGTTTAAATTCCTAATACA
GCCCCACTGAGTAAGAAACAAAGACAGAAAAGAACGCCTGTCAAAAGGCCAGAAACATAAGGCGGCCAGTAAAACTTCCT
CAAGGATGGATTTGGTTGATGGT

Alignment

ORF - retro_sscr_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.32 %
• Parental protein coverage: 90.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSANEDQEMELEALRSIYEGD-ESFRELSPVSF-QYRIGENGDPKAFLIEISWTETYPQTPPIISMNAFF
          ..A..D.E...E....I.EGD.E.F.ELSPVSF.....GE.GDPKAF..E.S.T.TYPQ..PI.SMNA.F
Retrocopy LGAKKDKEVGREVWHCIEEGD>ERF*ELSPVSF<SIGVGESGDPKAFFLELSGTDTYPQPLPISSMNASF

Parental  NNTISSAV-KQSILAKLQEAVEVNLGTAMTYTLFEYAKDNK-EQFMENHHPIHSAVSQTSISNIISTEAP
          .NT..SAV..QS..AKL.EAVEVNL..AMTYTL.EY.KD.K.EQFMEN.HP..S.....SIS.IIS...P
Retrocopy -NTVLSAV<QQSTEAKL*EAVEVNLRPAMTYTLSEYTKDKK<EQFMENYHPVNS---MSSISKIISV*IP

Parental  NTAPSSKK-KDKKEQLSKAQKRKLADKTDHKGELPRG
          NTAP.SKK.KD.KE.LSK.QK.K.A.KT.....L..G
Retrocopy NTAPLSKK>KDRKERLSKGQKHKAASKTSSRMDLVDG

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	11.81 RPM
SRP014902_testis	0.00 RPM	9.19 RPM
SRP018288_heart	0.00 RPM	20.48 RPM
SRP018288_kidney	0.00 RPM	24.82 RPM
SRP018288_liver	0.00 RPM	11.67 RPM
SRP018288_lung	0.00 RPM	14.87 RPM
SRP018856_adipose	0.00 RPM	14.49 RPM
SRP035408_brain	0.00 RPM	2.60 RPM
SRP035408_liver	0.00 RPM	7.02 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1019 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1019 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003081	1 retrocopy	retro_btau_603,
Canis familiaris	ENSCAFG00000007880	1 retrocopy	retro_cfam_1281,
Choloepus hoffmanni	ENSCHOG00000005290	3 retrocopies	retro_chof_1477, retro_chof_441, retro_chof_887,
Dasypus novemcinctus	ENSDNOG00000015132	1 retrocopy	retro_dnov_968,
Felis catus	ENSFCAG00000024337	1 retrocopy	retro_fcat_1156,
Homo sapiens	ENSG00000182552	2 retrocopies	retro_hsap_3770, retro_hsap_3841,
Gorilla gorilla	ENSGGOG00000011982	1 retrocopy	retro_ggor_2536,
Myotis lucifugus	ENSMLUG00000006800	1 retrocopy	retro_mluc_545,
Monodelphis domestica	ENSMODG00000004223	2 retrocopies	retro_mdom_1015, retro_mdom_251,
Nomascus leucogenys	ENSNLEG00000010733	1 retrocopy	retro_nleu_1898,
Otolemur garnettii	ENSOGAG00000016709	5 retrocopies	retro_ogar_1084, retro_ogar_1171, retro_ogar_1228, retro_ogar_2652, retro_ogar_2789,
Ochotona princeps	ENSOPRG00000015147	1 retrocopy	retro_opri_1002,
Pongo abelii	ENSPPYG00000015230	1 retrocopy	retro_pabe_3082,
Pan troglodytes	ENSPTRG00000016632	2 retrocopies	retro_ptro_1456, retro_ptro_2556,
Rattus norvegicus	ENSRNOG00000022500	1 retrocopy	retro_rnor_2930,
Sarcophilus harrisii	ENSSHAG00000011971	1 retrocopy	retro_shar_760,
Sus scrofa	ENSSSCG00000015776	2 retrocopies	retro_sscr_1019 , retro_sscr_1051,
Ictidomys tridecemlineatus	ENSSTOG00000013086	1 retrocopy	retro_itri_533,
Tarsius syrichta	ENSTSYG00000006599	1 retrocopy	retro_tsyr_1898,
Vicugna pacos	ENSVPAG00000005743	1 retrocopy	retro_vpac_341,