RetrogeneDB ID: retro_cpor_1189

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_54:10202212..10203175(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UAP1
• Ensembl ID: ENSCPOG00000004568
• Aliases: None
• Description: UDP-N-acteylglucosamine pyrophosphorylase 1 [Source:HGNC Symbol;Acc:12457]

Sequence

>retro_cpor_1189
CTTTTCCAGATTTTTTAGAACAAAGGAGCAGTTCCCCTGCTAGAAGATGGACAGAGGGCAACAGTTGGAATGGCATATCC
CAGAAGGAAGTGTGATGTGGGTTCACTATCCCATAAGACATTTTCAGATTTAGCAGAGTATGTCCTGAAGCTACAGCTGT
TAGCTAAAGCTATCATGGCCTCAAGTGGATCAGTCCATGCTAGATAGGGGCCAGTGGCAGAAAAACAGAAGTGTCAAAGG
AGTTCTTCATAAAACACAAGCACTTTGGTTGAAAAAAGAAAATGTAATCTATTTTGATCAGGGCATGCTGCCTGTTATGA
GTTTTAATGGGAAAATTCCTTTGGAAGAAAAGCACAAAATTTCTATGGCCCCAGATGGAAATGAGGTTTTTTTCAGGGTT
TTGCAGCCCAGGATATGGTGGAGGATGTGGAACAAAAAGGCACCTGGTGCACTTGCATCTGCTACGTGGATGATGCATTG
GTTAAAGTGAAGCCAATGGTTATTGAATTCCATGTTGAGAAAGGGCAGACTGTGGAGCAAAGATGATAGAGGAGATAACA
CTACAGAGCCAGGTGGAGTGGTTTGTGCGGTGATTGGTGGATAATGGGTGGTAGAATAGAGCAAAATTTCCCTGGCAACA
TCTCAGGTACGGAGCTCGGATGGACAAGTGCTGTTCTGTGTGGGCTGCATCACCAATCACATCTTCATCGTCCCATGTCT
GAGAGATGCTGTTGATGTTGATGAACCTCAGCTTTAGCGCCATCTGGCTCACAGGAAGATTCCATATGTGGATTCCTGGG
GTGAGTTAATTATGCCAGACAAGTCATGTGGAATAAATTGCCAAAAGTAGCTTCTGACATCTTCCAGATTGCAGAGAAGC
TTGCTGTGTATGAAGGTTTATCGGAGGATGGATTTTCCCAGCTAAAGGATGCAGACAGTCACAGTGGGAAGGACAACCCA
AGT

Alignment

ORF - retro_cpor_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.82 %
• Parental protein coverage: 62.26 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSHKTLFQIQAERILKLQLLAE-KYYGNKCIIPWY
          LFQI..NK.AV.LL..GQ....G.AYP....DVG..SHKT.F...AE..LKLQLLA...Y.G.K.I.P..
Retrocopy LFQIF*NKGAVPLLEDGQRATVGMAYPRRKCDVGSLSHKT-FSDLAEYVLKLQLLAK<SYHGLKWISPC*

Parental  IMTSGRTMEATKEFFTKHKYFG-LKKENIIFFQQGMLPAMSFDGKIILEEKNKVSMAPDGNG-GLYRALA
          I..SGR..E..KEFF.KHK.FG.LKKEN.I.F.QGMLP.MSF.GKI.LEEK.K.SMAPDGN..G.....A
Retrocopy IGASGRKTEVSKEFFIKHKHFG<LKKENVIYFDQGMLPVMSFNGKIPLEEKHKISMAPDGNE<GFFQGFA

Parental  AQNIVEDMEQRGIWCIHVYCVDNILVKVADPRFIGFCIQKG-ADCGAKVVEKT-NPTEPVGVVCRVDGVY
          AQ..VED.EQ.G.WC.....VD..LVKV..P..I.F...KG.ADCGAK..E...N.TEP.GVVC.V.G..
Retrocopy AQDMVEDVEQKGTWCTCICYVDDALVKVK-PMVIEFHVEKG<ADCGAKMIEEI<NTTEPGGVVCAVIGG*

Parental  QVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTIPFLRDVVNVYEPQLQHHVAQKKIPYVDSRGELIK
          .VVE.S.ISLAT.Q.RSSDG..LF..G.I.NH.F..P.LRD.V.V.EPQL..H.A..KIPYVDS.GELI.
Retrocopy WVVE*SKISLATSQVRSSDGQVLFCVGCITNHIFIVPCLRDAVDVDEPQL*RHLAHRKIPYVDSWGELIM

Parental  PDKPNGI-KMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPT
          PDK..GI.K..K...DIFQ.A.K..VYE.L.ED.FS.LK.ADS..GKDNP.
Retrocopy PDKSCGI<KLPKVASDIFQIAEKLAVYEGLSEDGFSQLKDADSHSGKDNPS

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	0.00 RPM	27.38 RPM
SRP017611_kidney	0.00 RPM	59.25 RPM
SRP017611_liver	0.00 RPM	29.25 RPM
SRP040447_lung	0.00 RPM	36.92 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1189 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1189 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004264	1 retrocopy	retro_cjac_2537,
Cavia porcellus	ENSCPOG00000004568	5 retrocopies	retro_cpor_1186, retro_cpor_1187, retro_cpor_1188, retro_cpor_1189 , retro_cpor_511,
Dasypus novemcinctus	ENSDNOG00000024661	1 retrocopy	retro_dnov_1035,
Macaca mulatta	ENSMMUG00000019514	1 retrocopy	retro_mmul_1238,
Rattus norvegicus	ENSRNOG00000002926	1 retrocopy	retro_rnor_2277,
Tarsius syrichta	ENSTSYG00000002725	3 retrocopies	retro_tsyr_121, retro_tsyr_390, retro_tsyr_582,