RetrogeneDB ID: retro_sscr_600

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 18:39569762..39570320(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000027662
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000026942
• Aliases: None
• Description: None

Sequence

>retro_sscr_600
AGGCAGCAAGCAACTGATGCAAGACCCTTTGAAGCAGACAATGCAAATGAATCATGGAGAACTTCAGTAGAAACGGCTCT
TCAAACTTATCTAAAAGAACATTATTCAAACTGAGTTTGCACTGTATATGTTAAAAAAAAAATAGATGAACAGCAAACCA
TTATTACATGCATAAAAAGCCATAAGTTTCAAGAAAAAAATTTTGGAATGGTCATTGGTGGTCAGAGTGGAAGTCTACAA
TCACTTCTTCAACCATTCAGGTGGCTGGCATCTTGAAAATTCAGGTTCATTATTATGAAGATAGTTAATGTTCAGCTAGT
GAGTCATAAAGATATACAAGATTCCCTAACAGCATCTAATGAGGTGCAAAGAGCAAAAGAATTTATAAAGATTGTAGAGG
CTGCAGAAAATGAGTATCAGACTATCATCATTAAGAATTATGAGACAACATCAGACACTACTTTCAAAGTCTTATGTCAA
GAGTTGCCAGCTACACACACAAGGACTGACTGGAACAAGATCCTTAGCCACAAGATTGGCATAGAGATGCAGAGTGCC

Alignment

ORF - retro_sscr_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 67.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKEATDPRPYEAENAVESWRTSVETALRAYVKEHYPNGVCTVY-GKKIDGQQTIIACIESHQFQAKNF-W
          R..ATD.RP.EA.NA.ESWRTSVETAL..Y.KEHY.N.VCTVY.....D.QQTII.CI.SH.FQ.KNF.W
Retrocopy RQQATDARPFEADNANESWRTSVETALQTYLKEHYSN*VCTVYVXXXXDEQQTIITCIKSHKFQEKNF<W

Parental  NGRWRSEWKFTITPSTTQVVGILKIQVHYYEDG-NVQLVSHKDIQDSLTVSNEVQTAKEFIKIVEAAENE
          NG.W.SEWK.TIT.ST.QV.GILKIQVHYYED..NVQLVSHKDIQDSLT.SNEVQ.AKEFIKIVEAAENE
Retrocopy NGHWWSEWKSTITSSTIQVAGILKIQVHYYEDS>NVQLVSHKDIQDSLTASNEVQRAKEFIKIVEAAENE

Parental  YQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA
          YQT.I..NY.T.SDTTFK.L...LP.T.T..DWNKILS.KIG.EMQ.A
Retrocopy YQTIIIKNYETTSDTTFKVLCQELPATHTRTDWNKILSHKIGIEMQSA

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	0.00 RPM
SRP014902_testis	0.00 RPM	0.00 RPM
SRP018288_heart	0.00 RPM	0.05 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.00 RPM
SRP018856_adipose	0.00 RPM	0.00 RPM
SRP035408_brain	0.06 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_600 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_600 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004925	2 retrocopies	retro_chof_2296, retro_chof_680,
Cavia porcellus	ENSCPOG00000007677	1 retrocopy	retro_cpor_205,
Dasypus novemcinctus	ENSDNOG00000005771	1 retrocopy	retro_dnov_1892,
Dipodomys ordii	ENSDORG00000016226	1 retrocopy	retro_dord_266,
Erinaceus europaeus	ENSEEUG00000009063	5 retrocopies	retro_eeur_142, retro_eeur_167, retro_eeur_351, retro_eeur_365, retro_eeur_482,
Echinops telfairi	ENSETEG00000019711	3 retrocopies	retro_etel_1516, retro_etel_2020, retro_etel_442,
Gorilla gorilla	ENSGGOG00000012158	1 retrocopy	retro_ggor_1774,
Microcebus murinus	ENSMICG00000000707	1 retrocopy	retro_mmur_1224,
Myotis lucifugus	ENSMLUG00000007910	1 retrocopy	retro_mluc_2595,
Oryctolagus cuniculus	ENSOCUG00000003591	2 retrocopies	retro_ocun_1531, retro_ocun_873,
Pongo abelii	ENSPPYG00000017933	1 retrocopy	retro_pabe_1321,
Sus scrofa	ENSSSCG00000026942	2 retrocopies	retro_sscr_1127, retro_sscr_600 ,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tupaia belangeri	ENSTBEG00000012657	2 retrocopies	retro_tbel_2004, retro_tbel_2228,