RetrogeneDB ID: retro_sscr_225

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:47592416..47592809(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030093
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAU
• Ensembl ID: ENSSSCG00000013002
• Aliases: None
• Description: Sus scrofa Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (FAU), mRNA. [Source:RefSeq mRNA;Acc:NM_213937]

Sequence

>retro_sscr_225
CAGCTCTTTGTCCCCGCCCAGGAGCTACATACTCTCGAGGTGACCGGCCAGGAGATGGTCGCCCAGATCAAGGCTCATGT
CGCCTTGTTGGAGGGCATCGCTCCGGAAGATCAAGTCCTGCTCTTGGCAGGCACGCCCCTGGAGGATGAGGCCATCCTCG
GCCAGTGTCGGGTGGAGGCCCTGAGCACTCTGGAAGTAGCCAGCCCTATGCTTGGAGGTAAAGTTCATGGTTCCCTGGCC
CGTGCTGGGAAAGTCAGAGATCAGACTCCCAAGGTGGCCAAACAAGAGAAAAAGAAGAAGACTGGCCGGGCCAAGAGACG
TATGCAATACAACGGGCGCTTTGTCAATGTCGTGCCCACCTTTGGCAAGAAGAAGGGACCCGATGCCAACTCT

Alignment

ORF - retro_sscr_225 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLFVRAQELHTLEVTGQETVAQIKAHVASLEGIAPEDQVLLLAGTPLEDDAILGQCGVEALSTLEVAGRM
          QLFV.AQELHTLEVTGQE.VAQIKAHVA.LEGIAPEDQVLLLAGTPLED.AILGQC.VEALSTLEVA..M
Retrocopy QLFVPAQELHTLEVTGQEMVAQIKAHVALLEGIAPEDQVLLLAGTPLEDEAILGQCRVEALSTLEVASPM

Parental  LGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTGRAKRRMQYNRRFVNVVPTFGKKKGPNANS
          LGGKVHGSLARAGKVR.QTPKVAKQE.KKKKTGRAKRRMQYN.RFVNVVPTFGKKKGP.ANS
Retrocopy LGGKVHGSLARAGKVRDQTPKVAKQE-KKKKTGRAKRRMQYNGRFVNVVPTFGKKKGPDANS

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	0.13 RPM	476.90 RPM
SRP014902_testis	0.42 RPM	613.74 RPM
SRP018288_heart	0.05 RPM	159.23 RPM
SRP018288_kidney	0.20 RPM	283.20 RPM
SRP018288_liver	0.32 RPM	335.81 RPM
SRP018288_lung	0.00 RPM	288.68 RPM
SRP018856_adipose	0.28 RPM	492.19 RPM
SRP035408_brain	0.67 RPM	333.90 RPM
SRP035408_liver	1.00 RPM	355.85 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_225 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017676	8 retrocopies	retro_amel_1, retro_amel_1065, retro_amel_1544, retro_amel_1806, retro_amel_1912, retro_amel_628, retro_amel_779, retro_amel_948,
Bos taurus	ENSBTAG00000020807	1 retrocopy	retro_btau_242,
Canis familiaris	ENSCAFG00000013934	7 retrocopies	retro_cfam_1162, retro_cfam_1598, retro_cfam_1734, retro_cfam_2190, retro_cfam_670, retro_cfam_750, retro_cfam_971,
Callithrix jacchus	ENSCJAG00000002432	1 retrocopy	retro_cjac_1935,
Dasypus novemcinctus	ENSDNOG00000004481	5 retrocopies	retro_dnov_1406, retro_dnov_1593, retro_dnov_1651, retro_dnov_1916, retro_dnov_2021,
Dipodomys ordii	ENSDORG00000003616	2 retrocopies	retro_dord_467, retro_dord_78,
Equus caballus	ENSECAG00000021956	2 retrocopies	retro_ecab_149, retro_ecab_951,
Echinops telfairi	ENSETEG00000010568	1 retrocopy	retro_etel_40,
Felis catus	ENSFCAG00000024367	9 retrocopies	retro_fcat_1163, retro_fcat_1281, retro_fcat_1777, retro_fcat_2008, retro_fcat_245, retro_fcat_349, retro_fcat_366, retro_fcat_420, retro_fcat_506,
Homo sapiens	ENSG00000149806	2 retrocopies	retro_hsap_1952, retro_hsap_2892,
Gorilla gorilla	ENSGGOG00000002714	1 retrocopy	retro_ggor_559,
Loxodonta africana	ENSLAFG00000001689	1 retrocopy	retro_lafr_1111,
Microcebus murinus	ENSMICG00000016596	2 retrocopies	retro_mmur_1534, retro_mmur_572,
Myotis lucifugus	ENSMLUG00000015370	3 retrocopies	retro_mluc_1070, retro_mluc_2324, retro_mluc_2390,
Macaca mulatta	ENSMMUG00000018776	1 retrocopy	retro_mmul_1453,
Monodelphis domestica	ENSMODG00000010095	1 retrocopy	retro_mdom_402,
Mustela putorius furo	ENSMPUG00000012237	1 retrocopy	retro_mputfur_144,
Mus musculus	ENSMUSG00000038274	1 retrocopy	retro_mmus_131,
Oryctolagus cuniculus	ENSOCUG00000014878	3 retrocopies	retro_ocun_139, retro_ocun_373, retro_ocun_939,
Otolemur garnettii	ENSOGAG00000015013	4 retrocopies	retro_ogar_146, retro_ogar_1491, retro_ogar_1724, retro_ogar_2545,
Pongo abelii	ENSPPYG00000003077	2 retrocopies	retro_pabe_2393, retro_pabe_3613,
Pan troglodytes	ENSPTRG00000003866	3 retrocopies	retro_ptro_1306, retro_ptro_1955, retro_ptro_1956,
Rattus norvegicus	ENSRNOG00000020982	3 retrocopies	retro_rnor_182, retro_rnor_314, retro_rnor_315,
Sarcophilus harrisii	ENSSHAG00000000131	1 retrocopy	retro_shar_523,
Sus scrofa	ENSSSCG00000013002	2 retrocopies	retro_sscr_225 , retro_sscr_464,
Ictidomys tridecemlineatus	ENSSTOG00000003336	1 retrocopy	retro_itri_1500,
Tupaia belangeri	ENSTBEG00000007492	11 retrocopies	retro_tbel_1550, retro_tbel_1735, retro_tbel_2045, retro_tbel_27, retro_tbel_2862, retro_tbel_301, retro_tbel_3396, retro_tbel_356, retro_tbel_3741, retro_tbel_3940, retro_tbel_4687,
Tarsius syrichta	ENSTSYG00000014667	16 retrocopies	retro_tsyr_1039, retro_tsyr_1041, retro_tsyr_1319, retro_tsyr_1325, retro_tsyr_1407, retro_tsyr_1436, retro_tsyr_1463, retro_tsyr_1474, retro_tsyr_1895, retro_tsyr_223, retro_tsyr_272, retro_tsyr_416, retro_tsyr_592, retro_tsyr_755, retro_tsyr_811, retro_tsyr_842,
Tursiops truncatus	ENSTTRG00000017246	6 retrocopies	retro_ttru_1163, retro_ttru_1221, retro_ttru_1248, retro_ttru_41, retro_ttru_798, retro_ttru_901,
Vicugna pacos	ENSVPAG00000005205	1 retrocopy	retro_vpac_304,