RetrogeneDB ID: retro_sscr_751

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:25279403..25279817(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D1
• Ensembl ID: ENSSSCG00000004020
• Aliases: None
• Description: SFT2 domain containing 1 [Source:HGNC Symbol;Acc:21102]

Sequence

>retro_sscr_751
CTGCGCACAGAGGTCCTAGATGCTCTGTCCCTTAGTTTTGACACCAAACTGAGGTGGTTTGGCATATGCTTTGTATGCAG
CATTTTCTGTTTTTTCCTTGGAACTGAATTGCTATGGCTTCCTGATAGAATAAAACTTTTTTACAGTATTTTATACCTTG
GAGAATAACCCCGCAATAGTCTGTAGGAGTTTTTAATGGGCTCCAGGAAGCAACTGAAGAAAACATTTGAAACAACTTTG
TTTGCAACAATTATTAATTATCCTTTTTGTTTCATATTTATCCTGCATGCTTCTTTTTGGTGACATAAGAAGGGAATGGC
CATATTACTGTCCTTGTGAGTGACTGGATACAGTCTACTATGCATCCCATGTGCAAGAGATGCAGTCATGAAATGCTACT
CTTCCGTCCTAACT

Alignment

ORF - retro_sscr_751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.47 %
• Parental protein coverage: 89.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LTAQVLDASTLSFNTRLKWFVICFVSGIFFSFLGTGLLWLPGGIKLF-AVFYTFGNIAALASTCF-LMGP
          L...VLDA..LSF.T.L.WF.ICFV..IF..FLGT.LLWLP..IKLF..VFYT..N..A.....F.LMG.
Retrocopy LRTEVLDALSLSFDTKLRWFGICFVCSIFCFFLGTELLWLPDRIKLF>TVFYTLENNPAIVCRSF<LMGS

Parental  VKQLKKMFETTRLLATIVMILCLVLTLCAALWWRKKGLALLFCILQFLSLTWYSLSYIPYARDAVIKCCS
          .KQLKK.FETT.....I....C....L.A..W..KKG.A.L......L..T.YSL..IP.ARDAV.KC.S
Retrocopy RKQLKKTFETTLFATIINYPFCFIFILHASFW*HKKGMAILLS----L*VTGYSLLCIPCARDAVMKCYS

Parental  SLLS
          S.L.
Retrocopy SVLT

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	33.98 RPM
SRP014902_testis	0.00 RPM	18.53 RPM
SRP018288_heart	0.00 RPM	18.47 RPM
SRP018288_kidney	0.00 RPM	64.03 RPM
SRP018288_liver	0.00 RPM	23.51 RPM
SRP018288_lung	0.00 RPM	26.37 RPM
SRP018856_adipose	0.00 RPM	53.63 RPM
SRP035408_brain	0.00 RPM	6.35 RPM
SRP035408_liver	0.00 RPM	8.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_751 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_751 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_546
Equus caballus	retro_ecab_1029

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009311	3 retrocopies	retro_amel_1244, retro_amel_1452, retro_amel_374,
Bos taurus	ENSBTAG00000002993	5 retrocopies	retro_btau_1458, retro_btau_1460, retro_btau_31, retro_btau_546, retro_btau_900,
Canis familiaris	ENSCAFG00000000811	2 retrocopies	retro_cfam_283, retro_cfam_551,
Equus caballus	ENSECAG00000019479	1 retrocopy	retro_ecab_1029,
Mus musculus	ENSMUSG00000073468	1 retrocopy	retro_mmus_164,
Oryctolagus cuniculus	ENSOCUG00000001200	1 retrocopy	retro_ocun_1492,
Otolemur garnettii	ENSOGAG00000006302	1 retrocopy	retro_ogar_1601,
Ochotona princeps	ENSOPRG00000003408	2 retrocopies	retro_opri_37, retro_opri_809,
Pongo abelii	ENSPPYG00000017165	1 retrocopy	retro_pabe_181,
Sus scrofa	ENSSSCG00000004020	1 retrocopy	retro_sscr_751 ,
Tupaia belangeri	ENSTBEG00000000045	2 retrocopies	retro_tbel_3277, retro_tbel_747,
Tursiops truncatus	ENSTTRG00000004447	2 retrocopies	retro_ttru_1353, retro_ttru_624,