RetrogeneDB ID: retro_sscr_569

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:49416697..49417281(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBAG9
• Ensembl ID: ENSSSCG00000006024
• Aliases: None
• Description: estrogen receptor binding site associated, antigen, 9 [Source:HGNC Symbol;Acc:3123]

Sequence

>retro_sscr_569
CTCACAGTTTTCAGTTATTTAAAAGTTAGTACTTGCCTAGCAACAGTATTCTCATTTCTGAAGAGATGAATTTGCAGATC
TGGCTGGGGACTGAGTTTAAGGGGAGCCTGAATAACTTTGCCAACTACAGTGGATAACTCATCAGTTCCTCAACGGACAG
CTGTTGAAGAGTGGGCCTCTGGGATGAAGACGCATCCACAAGGGTAAAGACTGAAGGAGGAAATGGGAATGTGGCAACAA
ACAAAATGCTTAGAACAACTGGAACCTGACTCTTTTAAAGACATGCCATCGGCTAAAAGGAAAACGCAGAAAATCATTAG
GAAGAGAGAAGCATGACCTTTTAGCATCCCAGTTGGTAGCACAGGTTTTACCAGTAGATTATTGACTTCACAAAGATACC
TTTTACTCATCGGTCTCCTGAATTAGGCGACTTGGATACCTGGCAGGAAAATACCAACGCATGGGAGGAAGAAGATGTGG
TCTGGCAAGCCGAAGATGTTCTTAGGCTGCAGAAGATAAAGAAACAAAGGAAGAAAAGGGAAAAGGAAGCACAACAGCTA
ATGAAGAAGGAAGAAAACAAAATT

Alignment

ORF - retro_sscr_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.35 %
• Parental protein coverage: 92.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ITQFRLFKVCTCLATVFSFLKRLICRSGRGRKLSGDQITLPTTVDYSSVPKQADVEEWTS-WDEDAPTSV
          .T.F...KV.TCLATVFSFLKR.ICRSG.G..L.G..ITLPTTVD.SSVP....VEEW.S.WDEDA.T.V
Retrocopy LTVFSYLKVSTCLATVFSFLKR*ICRSGWGLSLRGA*ITLPTTVDNSSVPQRTAVEEWAS<WDEDASTRV

Parental  KIEGGNGNVAT-QQNA-LEQLEPDYFKDMTPTIRKTQKIIIKKREPLNFGIPDGSTGFSSRLAATQ-DMP
          K.EGGNGNVAT..QNA.LEQLEPD.FKDM....RKTQK.II.KRE...F.IP.GSTGF.SRL...Q...P
Retrocopy KTEGGNGNVAT<KQNA<LEQLEPDSFKDMPSAKRKTQK-IIRKREA*PFSIPVGSTGFTSRLLTSQ<KIP

Parental  FIHQSPELGDLDTWQENTNAWEEEEDAAWQAEEVLRQQKIADREKRAAEQQRKKMEKEAQRL
          F.H.SPELGDLDTWQENTNAW.EEED..WQAE.VLR.QKI....K.........M.KE....
Retrocopy FTHRSPELGDLDTWQENTNAW-EEEDVVWQAEDVLRLQKIKKQRKKREKEAQQLMKKEENKI

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	7.96 RPM
SRP014902_testis	0.00 RPM	9.90 RPM
SRP018288_heart	0.00 RPM	26.17 RPM
SRP018288_kidney	0.00 RPM	46.99 RPM
SRP018288_liver	0.00 RPM	32.30 RPM
SRP018288_lung	0.00 RPM	29.33 RPM
SRP018856_adipose	0.00 RPM	11.74 RPM
SRP035408_brain	0.00 RPM	52.12 RPM
SRP035408_liver	0.00 RPM	65.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_569 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_569 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006190	1 retrocopy	retro_amel_1656,
Choloepus hoffmanni	ENSCHOG00000007848	5 retrocopies	retro_chof_1116, retro_chof_1455, retro_chof_1805, retro_chof_2245, retro_chof_751,
Cavia porcellus	ENSCPOG00000001059	1 retrocopy	retro_cpor_1185,
Dipodomys ordii	ENSDORG00000010177	2 retrocopies	retro_dord_418, retro_dord_91,
Equus caballus	ENSECAG00000009719	2 retrocopies	retro_ecab_211, retro_ecab_232,
Felis catus	ENSFCAG00000025490	1 retrocopy	retro_fcat_777,
Macropus eugenii	ENSMEUG00000014115	3 retrocopies	retro_meug_1871, retro_meug_2058, retro_meug_597,
Monodelphis domestica	ENSMODG00000004795	2 retrocopies	retro_mdom_261, retro_mdom_665,
Mus musculus	ENSMUSG00000022339	1 retrocopy	retro_mmus_3501,
Rattus norvegicus	ENSRNOG00000004220	2 retrocopies	retro_rnor_2914, retro_rnor_2980,
Sus scrofa	ENSSSCG00000006024	1 retrocopy	retro_sscr_569 ,
Ictidomys tridecemlineatus	ENSSTOG00000015326	1 retrocopy	retro_itri_1119,
Tursiops truncatus	ENSTTRG00000001745	2 retrocopies	retro_ttru_496, retro_ttru_672,