RetrogeneDB ID: retro_cpor_1186

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_54:10017507..10018471(+)
• 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_1186
CTTTTCCAGATTTCTCAGAACAAAGGAGCAGTTCCCCTGCTAGCAGATGGACAGAGGGCAACAGTTGGAATGGCATATCC
CGGAAGGAAGTGTGATGTGGTTTCACTATCCCATAAGACATTTTCAGATTCCAGCAGAGCATGTTCTGAAGCTACAGCTG
TTATCTAAAGCTATCATGGCTTCAAATGGATCAGTCCATGGTAGGTAGAGGCCAGTGGCAGAAAAATAGAAGAGACAAAG
GAGTTCTTCATAAAACACAAGTACTTTGGTTGAAAAAAGAAAATGTAATCTATTTTGATCAGGGCATGCTGCCTGCTATG
AGTTTTATGGGAAAATTACTTTGGAAGAAAAGAACAAAATTTCTATGGCCCCAGATGGAAATGAGGGTTTTTTTTGGGCT
TTGGCAGCCCAGAATATGGTGGAGGATTTGTATCAAAAAGGCACCTGGTGCACTTGCATCTGCTACGTGGATGATGCATT
GGTTAAAGTGAAGCCAATGGTTATTGAATTCCACGTTGAGAAAGGGCAGACTGTGGAGCAATGGTGATAGAGGAGAGAAC
ACTACAGAGCCAGGTGGAGTGGTTTGTTCCATGAATGGTGGATAATGGGTGGTAGAATAGAGCAAAATTTCCCTGGCAAC
ATCTCAGGTACGGAGCTCGGATGGACAAGTGCTGTTCTGTTTGGGCCGCATCACCAATCACATCTTCATCGTCCTATGTC
TGAGAGATGCTGTTGGTGTTGATGAACCTCAGCTTTAGCGCCATCTGGCTCACAGGAAGATTCCATATGTGGATTCCTGG
GGTGAGTTAATTATGCCAGACAAGTCATGTGGTATAAATTGCCAAAAGTAGCTTCTGACATCTTCCAGATTGCAGAGAAG
CTTGCGTTGTATGAAGGTTTATCGAAGGATGGATTTTCCCCGCTTAAGCATGCAGACAGTCACAGTGTGAAGGACAACCC
AAGT

Alignment

ORF - retro_cpor_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.06 %
• Parental protein coverage: 62.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  LFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSHKT-LFQIQ-AERILKLQLLAE-KYYGNKCIIP
          LFQISQNK.AV.LLA.GQ....G.AYP....DV...SHKT..F..Q.AE..LKLQLL....Y.G.K.I.P
Retrocopy LFQISQNKGAVPLLADGQRATVGMAYPGRKCDVVSLSHKT<IFRFQ<AEHVLKLQLLSK<SYHGFKWISP

Parental  WYIMTSGRTMEATKEFFTKHKYFG-LKKENIIFFQQGMLPAMSFDGKII-LEEKNKVSMAPDGNGGLYRA
          W....SGR..E.TKEFF.KHKYFG.LKKEN.I.F.QGMLPAMSF.GK...LEEKNK.SMAPDGN.....A
Retrocopy W*VEASGRKIEETKEFFIKHKYFG<LKKENVIYFDQGMLPAMSFMGKLL<LEEKNKISMAPDGNEXXXXA

Parental  LAAQNIVEDMEQRGIWCIHVYCVDNILVKVADPRFIGFCIQKG-ADCGAKVVEK-TNPTEPVGVVCRVDG
          LAAQN.VED..Q.G.WC.....VD..LVKV..P..I.F...KG.ADCGA.V.E...N.TEP.GVVC...G
Retrocopy LAAQNMVEDLYQKGTWCTCICYVDDALVKV-KPMVIEFHVEKG<ADCGAMVIEE<ENTTEPGGVVCSMNG

Parental  VYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTIPFLRDVVNVYEPQLQHHVAQKKIPYVDSRGEL
          ...VVE.S.ISLAT.Q.RSSDG..LF..G.I.NH.F....LRD.V.V.EPQL..H.A..KIPYVDS.GEL
Retrocopy G*WVVE*SKISLATSQVRSSDGQVLFCLGRITNHIFIVLCLRDAVGVDEPQL*RHLAHRKIPYVDSWGEL

Parental  IKPDKPNGI-KMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPT
          I.PDK..GI.K..K...DIFQ.A.K...YE.L..D.FSPLK.ADS...KDNP.
Retrocopy IMPDKSCGI<KLPKVASDIFQIAEKLALYEGLSKDGFSPLKHADSHSVKDNPS

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_1186 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1186 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,