RetrogeneDB ID: retro_sscr_825

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:72762389..72762867(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000000777
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000016152
• Aliases: None
• Description: None

Sequence

>retro_sscr_825
TTGCACGCTATGGTGTTCAGGCGGGAACAGTGGGTAAAGCCAATGGCTGTAGTGGGAACCAATCAATATACATTTCATCT
TGAAGCTACTGAGAACCCTGGGAGCTTTGATTAAAGACATTCAGGAGAATGATGAAGGCTGGCTTTGCTATCAAACTAGG
AACTATAGTTGAATATTTGGCACCATGGACTAATCAGATAGATATGGCCTTGGTTCTGACAGTGGAACGTGGGTTTGGAG
GGCAGAAATTCATGGAAGATATGATGCCAAAGATTCAGCGGTTGAGGACCCAGTTCCCTTCTTTGGACATAGAGGTTGAT
GGTGGAGTAGGTCCTGACACAATCCATAAATGTGCAGAGGCAGGAGCTAACATGATTGTGGCTGGCAGTGCCATTGTGAG
TAGTGAGACTCCAAATCTGTGATCAACCTGTTAAGAAATGTTTGCTCAGAAGCTGCTCAGAAACATTCTCTTGATCAA

Alignment

ORF - retro_sscr_825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MHMMVSRPEQWVKPMAVAGANQYTFHLEATENP-GAL-IKDIRENGMKVGLAIKPGTTVEYLAPWANQID
          .H.MV.R.EQWVKPMAV.G.NQYTFHLEATENP.GAL..K..R...MK.G.AIK.GT.VEYLAPW.NQID
Retrocopy LHAMVFRREQWVKPMAVVGTNQYTFHLEATENP>GAL>LKTFRRM-MKAGFAIKLGTIVEYLAPWTNQID

Parental  MALVMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTIHKCAEAGANMIVSGSAIMRSEDP
          MALV.TVE.GFGGQKFMEDMMPK...LRTQFPSLDIEVDGGVGPDTIHKCAEAGANMIV.GSAI..SE.P
Retrocopy MALVLTVERGFGGQKFMEDMMPKIQRLRTQFPSLDIEVDGGVGPDTIHKCAEAGANMIVAGSAIVSSETP

Parental  -RSVINLLRNVCSEAAQKRSLDR
          ..SVINLLRNVCSEAAQK.SLD.
Retrocopy <KSVINLLRNVCSEAAQKHSLDQ

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	1.46 RPM
SRP014902_testis	0.00 RPM	2.12 RPM
SRP018288_heart	0.00 RPM	0.73 RPM
SRP018288_kidney	0.00 RPM	3.05 RPM
SRP018288_liver	0.00 RPM	0.32 RPM
SRP018288_lung	0.00 RPM	1.02 RPM
SRP018856_adipose	0.03 RPM	4.94 RPM
SRP035408_brain	0.00 RPM	0.16 RPM
SRP035408_liver	0.00 RPM	0.38 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_825 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_825 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004965	3 retrocopies	retro_amel_1327, retro_amel_1363, retro_amel_827,
Bos taurus	ENSBTAG00000047806	2 retrocopies	retro_btau_343, retro_btau_815,
Canis familiaris	ENSCAFG00000013811	3 retrocopies	retro_cfam_1441, retro_cfam_1596, retro_cfam_1623,
Choloepus hoffmanni	ENSCHOG00000001110	5 retrocopies	retro_chof_1534, retro_chof_2386, retro_chof_392, retro_chof_492, retro_chof_574,
Callithrix jacchus	ENSCJAG00000010822	2 retrocopies	retro_cjac_1199, retro_cjac_1560,
Dasypus novemcinctus	ENSDNOG00000003193	1 retrocopy	retro_dnov_789,
Equus caballus	ENSECAG00000000002	3 retrocopies	retro_ecab_245, retro_ecab_446, retro_ecab_562,
Homo sapiens	ENSG00000197713	5 retrocopies	retro_hsap_133, retro_hsap_2553, retro_hsap_2620, retro_hsap_3330, retro_hsap_620,
Latimeria chalumnae	ENSLACG00000002800	1 retrocopy	retro_lcha_21,
Loxodonta africana	ENSLAFG00000014127	2 retrocopies	retro_lafr_675, retro_lafr_729,
Microcebus murinus	ENSMICG00000009953	4 retrocopies	retro_mmur_1380, retro_mmur_268, retro_mmur_393, retro_mmur_713,
Macaca mulatta	ENSMMUG00000010513	2 retrocopies	retro_mmul_366, retro_mmul_618,
Monodelphis domestica	ENSMODG00000015827	6 retrocopies	retro_mdom_1181, retro_mdom_1676, retro_mdom_449, retro_mdom_490, retro_mdom_505, retro_mdom_667,
Mustela putorius furo	ENSMPUG00000007948	2 retrocopies	retro_mputfur_1066, retro_mputfur_1280,
Nomascus leucogenys	ENSNLEG00000007172	3 retrocopies	retro_nleu_2263, retro_nleu_448, retro_nleu_638,
Oryctolagus cuniculus	ENSOCUG00000016995	1 retrocopy	retro_ocun_768,
Otolemur garnettii	ENSOGAG00000002778	1 retrocopy	retro_ogar_2673,
Pongo abelii	ENSPPYG00000013132	4 retrocopies	retro_pabe_1052, retro_pabe_1878, retro_pabe_2340, retro_pabe_555,
Pteropus vampyrus	ENSPVAG00000014452	2 retrocopies	retro_pvam_217, retro_pvam_636,
Sus scrofa	ENSSSCG00000016152	1 retrocopy	retro_sscr_825 ,
Ictidomys tridecemlineatus	ENSSTOG00000010322	1 retrocopy	retro_itri_1750,
Tarsius syrichta	ENSTSYG00000003304	5 retrocopies	retro_tsyr_113, retro_tsyr_1153, retro_tsyr_1663, retro_tsyr_2129, retro_tsyr_546,
Tursiops truncatus	ENSTTRG00000000908	1 retrocopy	retro_ttru_158,
Vicugna pacos	ENSVPAG00000011585	1 retrocopy	retro_vpac_91,