RetrogeneDB ID: retro_rnor_252

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:163127460..163128414(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000007740
• Aliases: Tacstd2, Prp1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Epcam
• Ensembl ID: ENSRNOG00000015667
• Aliases: Epcam, Egp314, Tacstd1
• Description: Epithelial cell adhesion molecule [Source:UniProtKB/Swiss-Prot;Acc:O55159]

Sequence

>retro_rnor_252
ATGGCGAGGGGCTTGGATCTAGCACCGCTGCTACTGCTACTGCTGGCGATGGTGGCCGGCTTTTGCACGGCCCAGATCAA
CTGCACATGCCCTACCAACAAGATGACCGTCTGCAACTCTAATGGCCCAGGTGGGGTCTGCCAATGTCGGGCAATCGGCT
CGCAGGTGTTGGTCGACTGCTCCACGCTAACTTCCAAGTGCCTGCTACTCAAGGCGCGCATGAGCGCCCGAAAGAGCAGC
CGCAGACTGGTGAATCCGAGCGAGCACGCGATCTTGGACAACGATGGCCTCTACGACCCGGAGTGTGACGACAAGGGCCG
CTTCAAGGCGCGCCAGTGCAACCAGACCTCGGTGTGCTGGTGCGTAAACTCGGTGGGCGTGCGCCGAACGGACAAGGGAG
ACCAGAGCCTGCGCTGCGACGAAGTGGTGCGAACCCACCACATCCTCATTGAGTTGCGCCACCGCCCGACAGACCGAGCC
TTCAACCACTCTGACCTAGACTCCGAGCTGCGGCGGCTCTTCAAGGAACGCTACAAGCTGCACCCCAGCTTCCTGGCCGC
GGTGCACTACGAAGAGCCCACCATCCAGATCGAGCTGCAGCAGAACGCGTCACAGAAGGGCCTGAGAGACGTGGACATCG
CTGACGCCGCCTACTACTTCGAAAGGGACATCAAAGGCGAGTCACTGTTCGTGGGCCGTCGCGGCCTGGACGTGCAGGTG
CGTGGGGAGCCCCTGCATGTGGAGCGGACTCTCATCTACTACCTGGACGAGAAGCCCCCCCAGTTCTCCATGAAGCGCCT
CACCACCGGCCTCATTGCCGTCATCGCTGTCGTCGCGGTGGCACTAGTGGCCGGTGTGGTGGTCTTGGTGGTCACCAACC
GGAGGAAATCAGGAAAATACAAAAAGGTGGAGCTTAAGGAGCTAGGGGAGATGAGAAGCGAACCTAGCTTGTAG

Alignment

ORF - retro_rnor_252 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.15 %
• Parental protein coverage: 95.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLAVVTATLAAAQKDCVCNNYKLTSRCYENENGECQCTSYGTQNTVICSKLASKCLVMKAEMTHSKSGR
          LLL....A....AQ..C.C...K.T........G.CQC...G.Q..V.CS.L.SKCL..KA.M...KS.R
Retrocopy LLLLAMVAGFCTAQINCTCPTNKMTVCNSNGPGGVCQCRAIGSQVLVDCSTLTSKCLLLKARMSARKSSR

Parental  RM--KPEGAIQNNDGLYDPECDEQGLFKAKQCNGTATCWCVNTAGVRRTDK-DTEITCSERVRTYWIIIE
          R.....E.AI..NDGLYDPECD..G.FKA.QCN.T..CWCVN..GVRRTDK.D....C.E.VRT..I.IE
Retrocopy RLVNPSEHAILDNDGLYDPECDDKGRFKARQCNQTSVCWCVNSVGVRRTDKGDQSLRCDEVVRTHHILIE

Parental  LKHKERAQPYNFESLHTALQDTFASRYMLNPKFIKSIMYENNVITIDLMQNSSQKTQDDVDIADVAYYFE
          L.H.......N...L...L...F..RY.L.P.F.....YE...I.I.L.QN.SQK...DVDIAD.AYYFE
Retrocopy LRHRPTDRAFNHSDLDSELRRLFKERYKLHPSFLAAVHYEEPTIQIELQQNASQKGLRDVDIADAAYYFE

Parental  KDVKGESLFHSSKSMDLRVNGELLDLDPGQTLIYYVDEKAPEFSMQGLTAGIIAVIVVVVLAVIAGIVVL
          .D.KGESLF......D..V.GE.L......TLIYY.DEK.P.FSM..LT.G.IAVI.VV..A..AG.VVL
Retrocopy RDIKGESLFVGRRGLDVQVRGEPLHVE--RTLIYYLDEKPPQFSMKRLTTGLIAVIAVVAVALVAGVVVL

Parental  VISTRKRSAKYEKAEIKEMGEIHRE
          V...R..S.KY.K.E.KE.GE...E
Retrocopy VVTNRRKSGKYKKVELKELGEMRSE

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
SRP017611_brain	0.07 RPM	0.86 RPM
SRP017611_kidney	5.86 RPM	433.21 RPM
SRP017611_liver	0.00 RPM	12.71 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_252 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_252 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_185

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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,