RetrogeneDB ID: retro_sscr_1153

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:43589396..43590383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006063
• Aliases: None
• Description: None

Sequence

>retro_sscr_1153
GACCTGCACTGGGAAGCGACCGAGGCGATGCTCTAGGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTG
CAGGGACGTGACCACCCGCCACTCCTTGGGCGCGGAGGTGAACTTCCAGCAGCCGACGGACACGGAGCGTGCTTTGAACA
CCCTGAACTTTGATGTTATAAAGGGCAAGCCAGCACGCATCCTGTGGTCTCTGCGTGATCCATCACTTTGCCAAAGTGGA
GTGGGCAACATTCATTTAAAACACTTGGACAGATCCATTGATAATAATAAAGCACTGTATGAGATGTTTTCTGCTCTTGG
TAACATCCTTTCATGTAAGGTGGTTTGTGATGAAAACGGTCCCAAGGGTTATGGATTTGTGCGCTTGGAGACACACGAAG
CAACTGAAAGAGCTATTGAAAAAAATGAATGGGATGCTTCTAAATGACGACAAAGCATTTGTTGGACGAGTTAAGTCTCT
TAAGGAATGAGAAGCAGACCTTGGAGTTAGGGCAAAGGAGTTCATCAAAGTTTACATCAAGAATTTTGGAGAAGACATGG
ATGATGAGCTCTTTAAGGATCTCTTTGGCAAGTTTGGACCTCCCTTGCCTGTGACAGCAATGACTGATGAGCGTGGACAA
TCCGAAGGTTTTGGATTTGCAAGCTTTGAAAGGCATGACGATGCGCAGAAAGCTGTGGATGAGATGAATGGAAAGGAGCT
CAGTGGAAAACACATGTATGTTGGTTGAGCCCAGAAAAAAGGGAAGGGCAGAGGGAACTTCAGCACAAATTTGAACAGAT
GAAGCAAGATGGGATCACCAGAGACCAGGGCGTTAACCTTTATGTGAAAAATCTTGATGATGGTTTTGATGATATATGTC
TCCGGAAGGAGCTTTCTCCATTTGGTACAATCACTAGTGCAAAGGTTATGATGGAGGGTGGTTGCAGCAACGGTCTTGGT
TTGGTATGTGTCTCCTCCCCAGAAGAA

Alignment

ORF - retro_sscr_1153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 51.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW
          DLH...TEAML.EKFSPAGPILSIRVCRD..TR.SLG.A.VNFQQP.D.ERAL.T.NFDVIKGKP.RI.W
Retrocopy DLHWEATEAML*EKFSPAGPILSIRVCRDVTTRHSLG-AEVNFQQPTDTERALNTLNFDVIKGKPARILW

Parental  SQRDPSLRKSGVGNIFIKNLDKSIDN-KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI
          S.RDPSL..SGVGNI..K.LD.SIDN.KALY..FSA.GNILSCKVVCDENG.KGYGFV..ET.EA.ERAI
Retrocopy SLRDPSLCQSGVGNIHLKHLDRSIDNNKALYEMFSALGNILSCKVVCDENGPKGYGFVRLETHEATERAI

Parental  EK-MNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMT
          EK.MNGMLLND.K.FVGR.KS.KE.EA.LG.RAKEF..VYIKNFGEDMDDE..KDLFGKFGP.L.V..MT
Retrocopy EK>MNGMLLNDDKAFVGRVKSLKE*EADLGVRAKEFIKVYIKNFGEDMDDELFKDLFGKFGPPLPVTAMT

Parental  DESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQK-KVERQTELKRKFEQMKQDRITRYQG
          DE.G.S.GFGF.SFERH.DAQKAVDEMNGKEL.GK..YVG.AQK.K.E.Q.EL..KFEQMKQD.ITR.QG
Retrocopy DERGQSEGFGFASFERHDDAQKAVDEMNGKELSGKHMYVG*AQK<KREGQRELQHKFEQMKQDGITRDQG

Parental  VNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEE
          VNLYVKNLDDG.DD..LRKE.SPFGTITSAKVMMEGG.S.G.G.VC.SSPEE
Retrocopy VNLYVKNLDDGFDDICLRKELSPFGTITSAKVMMEGGCSNGLGLVCVSSPEE

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	902.97 RPM
SRP014902_testis	0.14 RPM	607.37 RPM
SRP018288_heart	0.00 RPM	245.70 RPM
SRP018288_kidney	0.00 RPM	320.44 RPM
SRP018288_liver	0.00 RPM	408.09 RPM
SRP018288_lung	0.00 RPM	1054.61 RPM
SRP018856_adipose	0.03 RPM	862.54 RPM
SRP035408_brain	0.00 RPM	558.09 RPM
SRP035408_liver	0.00 RPM	472.86 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1153 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153 , retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,