RetrogeneDB ID: retro_sscr_975

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:98244990..98245950(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSSSCG00000003660
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_sscr_975
TACGTGAATTTCCTGCAGCTGGCAGATGCTCTGAAGGCCCTGGACACCATGAATTTTGACCTGATAAAAGGCAAATCCAT
CCGTCTCATGTGGTCTCAACGTGATGCCTACTTAAGGAAATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAAAT
CCATCGATAATAAAACCCTTTATGAACATTTTTCAGCTTTTGGGAAAATCCTGTCCTCCAAGGTGATGAGTGATGATCAG
GGCTCCAGGGGCTATGCATTTGTGCACTTTCAGAACCAGATTGCTGCAGACAGAGCCATCGAGGAGATGAATGGGGCACT
GCTTAAAGACTGCAGGCTGTTTGTTGGCAGATTCAAAAACCGCAAAGATCGAGAAGCAGAGCTTCAAAACAAAGCCAATG
AGTTCACCAATGTTTACATCAAAAACTTCGGAGATGACATGGATGATGAGAGACTGAAGGAAGTTTTCAGCAAATATGGC
AAAACCTTGAGTGTTAAGGTGATGAGAGATTCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCATGA
GGCTGCCAAAAAGGCTGTTGAAGAAATGAATGGAAAGGACATAAATGGACAGCTGCTTTTTGTAGGCCGGGCACAAAAGA
AAGCAGAGCGACAGGCTGAGTTAAAGCAAATGTTTGAGCAGCTGAAACGTGAAAGGTTTCGCCGGTGCCAGGGGGTAAAG
CTCTATATTAAGAACTTGGATGAGACCATTGATGATGAAAAACTACGGAGGGAATTTTCTTCATTTGGATCAATTAGCAG
AGTTAAGGTAATGCAGGAAGAAGGGCGAAGCAAAGGGTTTGGCTTGATCTGCTTCTCCTCTCCTGAGGAGGCCACTAAAG
CGATGACTGAGATGAATGGCCGCATCTTGGGCTCTAAGCCACTCAATATCGCCCTGGCCCAGAAGCCCTAGGACAGGAAA

Alignment

ORF - retro_sscr_975 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.31 %
• Parental protein coverage: 50.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YVNFQQPADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNI
          YVNF.Q.ADA..ALDTMNFD.IKGK.IR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FSAFG.I
Retrocopy YVNFLQLADALKALDTMNFDLIKGKSIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKTLYEHFSAFGKI

Parental  LSCKVVCDENGSKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYI
          LS.KV..D..GS.GYAFVHF..Q.AAD.AIE.MNG.LL.D...FVGRFK.RK.REAEL..KA.EFTNVYI
Retrocopy LSSKVMSDDQGSRGYAFVHFQNQIAADRAIEEMNGALLKDCRLFVGRFKNRKDREAELQNKANEFTNVYI

Parental  KNFGEEVDDENLKELFSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGR
          KNFG...DDE.LKE.FS..GKTLSVKVMRD.SGKSKGFGFVS...HE.A.KAVEEMNGK.I.G...FVGR
Retrocopy KNFGDDMDDERLKEVFSKYGKTLSVKVMRDSSGKSKGFGFVSFDSHEAAKKAVEEMNGKDINGQLLFVGR

Parental  AQKKVERQAELKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGF
          AQKK.ERQAELK..FEQLK.ER..R.QGV.LYIKNLD.TIDDEKLR.EFS.FGSI...KVM.E.GRSKGF
Retrocopy AQKKAERQAELKQMFEQLKRERFRRCQGVKLYIKNLDETIDDEKLRREFSSFGSISRVKVMQEEGRSKGF

Parental  GFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERK
          G..CFSSPEEATKA.TEMNGRI.GSKPL..ALAQ....RK
Retrocopy GLICFSSPEEATKAMTEMNGRILGSKPLNIALAQKP*DRK

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	231.22 RPM
SRP014902_testis	0.00 RPM	201.70 RPM
SRP018288_heart	0.05 RPM	115.04 RPM
SRP018288_kidney	0.10 RPM	59.20 RPM
SRP018288_liver	0.00 RPM	85.23 RPM
SRP018288_lung	0.10 RPM	48.16 RPM
SRP018856_adipose	0.00 RPM	136.76 RPM
SRP035408_brain	0.00 RPM	63.71 RPM
SRP035408_liver	0.00 RPM	96.90 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_975 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_975 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_975 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
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	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,