RetrogeneDB ID: retro_sscr_97

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:10735469..10735712(+)
• Located in intron of: ENSSSCG00000022710

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000003261
• Aliases: None
• Description: None

Sequence

>retro_sscr_97
AGAACAGCTGCCTTCCTCAAGAACGCCTGGGCCAGCGAGCCGGTGCTGGTGGCGGCCTTCACCTTGGGGGCCTCACTATA
ACTCTGCCCGTGCTCAGCCCCGACACGCTAGGCCCCCGTGATCAACGAGGACACAACCTACACCTACCCAGCGTCCCTCC
AAGACGACGGAAACATGCCTGACGTGCCCAGCCACCTCCAGGACCATCCCCAGGGACCAAACTGGGAGTGGCTGAAGAAC
CTG

Alignment

ORF - retro_sscr_97 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 96.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RIASFLKNAWAKEPVLVASFAIGGLAIILPSLSPYTNYAIRINRATPYNYPVPLRDDGNMPDVPSHPQD-
          R.A.FLKNAWA.EPVLVA.F..G......P...P.T..A..IN..T.Y.YP..L.DDGNMPDVPSH.QD.
Retrocopy RTAAFLKNAWASEPVLVAAFTLGASL*LCPCSAP-TR*APVINEDTTYTYPASLQDDGNMPDVPSHLQDH

Parental  PQGPSLEWLKNL
          PQGP..EWLKNL
Retrocopy PQGPNWEWLKNL

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	34.64 RPM
SRP014902_testis	0.00 RPM	32.96 RPM
SRP018288_heart	0.03 RPM	50.89 RPM
SRP018288_kidney	0.00 RPM	61.86 RPM
SRP018288_liver	0.00 RPM	24.15 RPM
SRP018288_lung	0.00 RPM	20.67 RPM
SRP018856_adipose	0.09 RPM	14.40 RPM
SRP035408_brain	0.00 RPM	20.52 RPM
SRP035408_liver	0.00 RPM	9.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_97 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_97 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_97 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007754	2 retrocopies	retro_btau_207, retro_btau_986,
Canis familiaris	ENSCAFG00000002703	4 retrocopies	retro_cfam_1103, retro_cfam_12, retro_cfam_1274, retro_cfam_695,
Callithrix jacchus	ENSCJAG00000018518	5 retrocopies	retro_cjac_188, retro_cjac_2215, retro_cjac_2526, retro_cjac_382, retro_cjac_92,
Cavia porcellus	ENSCPOG00000021937	1 retrocopy	retro_cpor_991,
Equus caballus	ENSECAG00000015897	3 retrocopies	retro_ecab_253, retro_ecab_598, retro_ecab_834,
Felis catus	ENSFCAG00000003611	6 retrocopies	retro_fcat_122, retro_fcat_1501, retro_fcat_442, retro_fcat_448, retro_fcat_839, retro_fcat_916,
Gorilla gorilla	ENSGGOG00000023650	2 retrocopies	retro_ggor_100, retro_ggor_1166,
Loxodonta africana	ENSLAFG00000018014	2 retrocopies	retro_lafr_225, retro_lafr_459,
Macropus eugenii	ENSMEUG00000002939	2 retrocopies	retro_meug_408, retro_meug_688,
Monodelphis domestica	ENSMODG00000004118	1 retrocopy	retro_mdom_404,
Mustela putorius furo	ENSMPUG00000010317	3 retrocopies	retro_mputfur_1070, retro_mputfur_124, retro_mputfur_771,
Mus musculus	ENSMUSG00000035674	3 retrocopies	retro_mmus_1843, retro_mmus_3244, retro_mmus_486,
Otolemur garnettii	ENSOGAG00000006931	10 retrocopies	retro_ogar_1056, retro_ogar_1244, retro_ogar_1260, retro_ogar_1990, retro_ogar_2128, retro_ogar_2732, retro_ogar_2970, retro_ogar_3105, retro_ogar_3427, retro_ogar_729,
Pan troglodytes	ENSPTRG00000028890	5 retrocopies	retro_ptro_1032, retro_ptro_1093, retro_ptro_1336, retro_ptro_255, retro_ptro_842,
Pteropus vampyrus	ENSPVAG00000015560	5 retrocopies	retro_pvam_1197, retro_pvam_1261, retro_pvam_479, retro_pvam_512, retro_pvam_979,
Rattus norvegicus	ENSRNOG00000014224	1 retrocopy	retro_rnor_104,
Sarcophilus harrisii	ENSSHAG00000009016	2 retrocopies	retro_shar_167, retro_shar_207,
Sus scrofa	ENSSSCG00000003261	3 retrocopies	retro_sscr_45, retro_sscr_628, retro_sscr_97 ,
Ictidomys tridecemlineatus	ENSSTOG00000025377	2 retrocopies	retro_itri_1280, retro_itri_756,