RetrogeneDB ID: retro_sscr_69

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:141453749..141454721(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000003832
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TACSTD1
• Ensembl ID: ENSSSCG00000008429
• Aliases: EPCAM, EGP, Ep-CAM, TACSTD1
• Description: Sus scrofa epithelial cell adhesion molecule (EPCAM), mRNA. [Source:RefSeq mRNA;Acc:NM_214419]

Sequence

>retro_sscr_69
ATGGCCCGGGGCCCGGGCCTCGCGCTGCTGTCGTTGTCGCTGCTGCCGCCGCTCCTGCTGCTGGTGGCGGTGATCGGCCA
CGCAGCCGCGCAGGACAACTGTACGTGCCCCACCAACAAGATGACCATGTGCGAAAGGAGCGGCCCGGGCGGCCGCTGCC
AGTGCCGCGCGCTCGGCTCAGGCCTGCTGGTCGACTGCTCCACGCTCACGTCCAAGTGTCTGCTGCTCAAGGCGCGCATG
AGCGCGTCCAAGAGCGGCCGCGCGCTGGTGCGTCCGAGCGAGCACGCGCTCGTGGACAACGACGGCCTGTACGACCCGGA
TTGCGACCAGCAGGGCAGCTTCAAGGCGCGCCAGTGCAACCAGACGTCCGTGTGCTGGTGCGTGAACTCGGTGGGCGTGC
GCCGCACCGACAAGGGCGACCAGAGCCTGCGCTGCGACGAGCTGGTGCGCACCCACCACATCCTCATCGACCTGCGCCAC
CGCCCGGACACCCGCGCCTTCAACCACTCGGACCTGGACGCCGAGCTGCGGCGGCTCTTCCGGGAGCGCTACCTGCTGCA
CCCCAAGTTCGTGGCTGCAGTGCATTACGAGCACCCCACCATTCAGATCGAGCTGCAGCAGAACGCGTCGCAGAAGGCCG
CCGGCGACGTGGACATCGCCGATGCAGCCTACTACTTCGAGAGGGACGTCAAGGGCGAGTCGGTGTTCCCTGGCCGCGGC
GGCCTAGACGTGCGCGTGCGCGGAGAGCCCCTGCTGCTGGAGCGGACGCTCATCTACTACCTGGACGAGAAGCCCCCCCA
GTTCTCCATGAAGCGCCTCACCAGCGGCCTCATCGCCGTCATCGTCGTGGTCGCGGTGGCCCTCGTCGCCGGCGTGGTTG
TCCTGGTGGTTACCAACCGGAGGAAGTCTGGGAAATACAAGAAGGTGGAGGTCAAGGAACTGGGGGAGATGAGAAAGGAA
CCGAGCTTGTAG

Alignment

ORF - retro_sscr_69 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.82 %
• Parental protein coverage: 95.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLAAATAAVAAAQQGCVCENYKLTTNCSLNALGQCQCTSIGAQNSVICSKLASKCLVMKAEMTGSKAGR
          LLL..A....AAAQ..C.C...K.T........G.CQC...G....V.CS.L.SKCL..KA.M..SK.GR
Retrocopy LLLLVAVIGHAAAQDNCTCPTNKMTMCERSGPGGRCQCRALGSGLLVDCSTLTSKCLLLKARMSASKSGR

Parental  RL-KP-ENAIQNNDGLYDPDCDENGLFKAKQCNGTSMCWCVNTAGVRRTDK-DSEISCLERVRTYWIIIE
          .L..P.E.A...NDGLYDPDCD..G.FKA.QCN.TS.CWCVN..GVRRTDK.D....C.E.VRT..I.I.
Retrocopy ALVRPSEHALVDNDGLYDPDCDQQGSFKARQCNQTSVCWCVNSVGVRRTDKGDQSLRCDELVRTHHILID

Parental  LKHKTREKPYDVTSLQNALKEVITDRYQLDPKYITNILYENDIITIDLVQNSSQKTLNEVDIADVAYYFE
          L.H...........L...L......RY.L.PK......YE...I.I.L.QN.SQK....VDIAD.AYYFE
Retrocopy LRHRPDTRAFNHSDLDAELRRLFRERYLLHPKFVAAVHYEHPTIQIELQQNASQKAAGDVDIADAAYYFE

Parental  KDVKDESLFHSK-RMDLRVNGELLDLDPGQTSIYYVDEKPPEFSMQGLQAGIIAVIAVVAIAIVAGIIVL
          .DVK.ES.F......D.RV.GE.L.L....T.IYY.DEKPP.FSM..L..G.IAVI.VVA.A.VAG..VL
Retrocopy RDVKGESVFPGRGGLDVRVRGEPLLLE--RTLIYYLDEKPPQFSMKRLTSGLIAVIVVVAVALVAGVVVL

Parental  IVSTKKRRAKYEKAEIKEMGEMHRE
          .V.......KY.K.E.KE.GEM..E
Retrocopy VVTNRRKSGKYKKVEVKELGEMRKE

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	2222.98 RPM	263.21 RPM
SRP014902_testis	0.42 RPM	0.57 RPM
SRP018288_heart	0.13 RPM	0.10 RPM
SRP018288_kidney	2.27 RPM	174.55 RPM
SRP018288_liver	0.16 RPM	2.72 RPM
SRP018288_lung	23.01 RPM	91.03 RPM
SRP018856_adipose	0.41 RPM	0.26 RPM
SRP035408_brain	1.02 RPM	0.83 RPM
SRP035408_liver	0.00 RPM	6.52 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

3 EST(s) were mapped to retro_sscr_69 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BI402685	141454002	141454366	100	364	0	364
CO987558	141454002	141454383	99.8	380	1	379
EW108090	141453672	141454067	100	395	0	395

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_69 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_69 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_92
Macaca mulatta	retro_mmul_34
Callithrix jacchus	retro_cjac_3006
Bos taurus	retro_btau_66

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006474	1 retrocopy	retro_btau_66,
Choloepus hoffmanni	ENSCHOG00000013834	1 retrocopy	retro_chof_258,
Callithrix jacchus	ENSCJAG00000000624	1 retrocopy	retro_cjac_3006,
Dasypus novemcinctus	ENSDNOG00000011799	1 retrocopy	retro_dnov_345,
Erinaceus europaeus	ENSEEUG00000009462	1 retrocopy	retro_eeur_151,
Macropus eugenii	ENSMEUG00000015074	2 retrocopies	retro_meug_1984, retro_meug_474,
Microcebus murinus	ENSMICG00000000151	1 retrocopy	retro_mmur_739,
Macaca mulatta	ENSMMUG00000012390	1 retrocopy	retro_mmul_34,
Monodelphis domestica	ENSMODG00000001077	1 retrocopy	retro_mdom_104,
Mus musculus	ENSMUSG00000045394	1 retrocopy	retro_mmus_185,
Ochotona princeps	ENSOPRG00000004301	1 retrocopy	retro_opri_1225,
Pelodiscus sinensis	ENSPSIG00000015680	1 retrocopy	retro_psin_22,
Pan troglodytes	ENSPTRG00000011902	1 retrocopy	retro_ptro_92,
Rattus norvegicus	ENSRNOG00000015667	1 retrocopy	retro_rnor_252,
Sus scrofa	ENSSSCG00000008429	1 retrocopy	retro_sscr_69 ,
Ictidomys tridecemlineatus	ENSSTOG00000008631	1 retrocopy	retro_itri_106,
Tursiops truncatus	ENSTTRG00000004235	2 retrocopies	retro_ttru_21, retro_ttru_394,