RetrogeneDB ID: retro_sscr_143

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:282040163..282040586(+)
• Located in intron of: ENSSSCG00000005453

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000011113
• Aliases: None
• Description: None

Sequence

>retro_sscr_143
ATTATCCTGGTGGAGCAGTTCCAACCACCAATGGGAGGCTTCTACCTAGATTCTCTGCAGGTGTCATGGATGGTAAGGAA
AGCCTGGAGGCACCTGATCTTTGGGAGCGTGAGTAAGAGACTGGCTTTAAAGTTGATGTTGCTGAATGTTCTCCCATTGA
ACATCTGCGTCCAGGCTTGTCAAAGTGTACCACACATATTATGATGGTAACTATTAATGGAGATGATGCTGAAAGTGTAA
GACATAAGCCAAAGCCAGCGGCTATAGAATCGCAGAAGTCATTTCTCTACCAAAGAACCACCTGCTGAACAGACTTGACA
CTCCAGTGGCTAAGAACATTTGAGAGTGGAGACCGGAGTCATGTCCTGGGCTCTGGCACTGAGACATGCATACGTGGAGC
CGTCTGAAGTGCCCTTTCTGAAA

Alignment

ORF - retro_sscr_143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.69 %
• Parental protein coverage: 64.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVLVKQFRPPMGGYCLE-FPAGLIDENESPEAAALRELEEETGYKGDVAECSPAVCMDPGLSNCTTHVVT
          ..LV.QF.PPMGG..L..F.AG..D..ES.EA..L.E.E.ETG.K.DVAECSP.....PGLS.CTTH...
Retrocopy IILVEQFQPPMGGFYLD<FSAGVMDGKESLEAPDLWERE*ETGFKVDVAECSPIEHLRPGLSKCTTHIMM

Parental  VMINGDDAENVRPKPKPGDGE-FVEVISLPKNDLLSRLHALVAD-EHLTVDARVYSYALALKHANTKPFE
          V.INGDDAE.VR.KPKP...E...EVISLPKN.LL.RL...VA..EHL.V...V.S.ALAL.HA...P.E
Retrocopy VTINGDDAESVRHKPKPAAIE<IAEVISLPKNHLLNRLDTPVAK<EHLRVETGVMSWALALRHAYVEPSE

Parental  VPFLK
          VPFLK
Retrocopy VPFLK

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	14.73 RPM
SRP014902_testis	0.00 RPM	13.30 RPM
SRP018288_heart	0.00 RPM	1.44 RPM
SRP018288_kidney	0.00 RPM	14.68 RPM
SRP018288_liver	0.00 RPM	7.84 RPM
SRP018288_lung	0.00 RPM	7.84 RPM
SRP018856_adipose	0.00 RPM	17.61 RPM
SRP035408_brain	0.00 RPM	5.91 RPM
SRP035408_liver	0.00 RPM	5.55 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_143 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019509	2 retrocopies	retro_btau_1326, retro_btau_1438,
Canis familiaris	ENSCAFG00000004794	2 retrocopies	retro_cfam_435, retro_cfam_612,
Equus caballus	ENSECAG00000023658	1 retrocopy	retro_ecab_647,
Echinops telfairi	ENSETEG00000006403	1 retrocopy	retro_etel_946,
Felis catus	ENSFCAG00000025093	1 retrocopy	retro_fcat_350,
Homo sapiens	ENSG00000165609	1 retrocopy	retro_hsap_3580,
Gorilla gorilla	ENSGGOG00000006325	1 retrocopy	retro_ggor_2415,
Loxodonta africana	ENSLAFG00000012052	1 retrocopy	retro_lafr_226,
Myotis lucifugus	ENSMLUG00000010453	2 retrocopies	retro_mluc_1263, retro_mluc_2073,
Macaca mulatta	ENSMMUG00000017141	1 retrocopy	retro_mmul_1828,
Nomascus leucogenys	ENSNLEG00000012298	1 retrocopy	retro_nleu_2838,
Oryctolagus cuniculus	ENSOCUG00000009308	1 retrocopy	retro_ocun_862,
Otolemur garnettii	ENSOGAG00000005816	2 retrocopies	retro_ogar_2071, retro_ogar_2988,
Pongo abelii	ENSPPYG00000002091	2 retrocopies	retro_pabe_2949, retro_pabe_3040,
Pan troglodytes	ENSPTRG00000002294	1 retrocopy	retro_ptro_2427,
Rattus norvegicus	ENSRNOG00000017741	1 retrocopy	retro_rnor_1672,
Sus scrofa	ENSSSCG00000011113	1 retrocopy	retro_sscr_143 ,
Tursiops truncatus	ENSTTRG00000007394	2 retrocopies	retro_ttru_209, retro_ttru_495,