RetrogeneDB ID: retro_cpor_363

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_132:1612225..1613013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSCPOG00000002066
• Aliases: None
• Description: None

Sequence

>retro_cpor_363
ATGGATTTATCAGGAGTGAAAAAGAAGAGCTTGCTAGGATTCAAAGACAATAATGAAAAATCCAGCATTAGGGCTCCTTC
TTCTACCAAATGCAAGGACCGCTCTGATGACAAGTCCATGGATCACTCTAAAGACAAAGAGGTCACCAAGGAGTCTAGTG
AGAAGGACTGCAGCAGGCCTAAGACCTGGAAGAGAGGCAGTGCTTCCAGTGGAAGCAGCAGCACTGTCTCAACTTCCAGT
TCTAACTGTAGCACCAATGCAGGCTCAAGCAGCAGCTCCAGTGTCTCTTTAGCATCCAGCTGCCCTGGAAGCTCCCGTAT
CTCTCACAGCTCTAGTTCCAGCAGCTCCTCTGGCTCCTCAAGCCCTTCTCCGTGCAGACGTGACAACAGGCGGCGCTCCC
ACTCCAAATCCAAACCACCTAAAAGAGGTGAAAAGGAGAGGAAAAGGTGAAGCTTTCGCCTAAACCCACCAAAGTGCACA
TTGGGAGGCTTACCAGGAATTATACTTTGGCTGTATTTTCCACCTATGGGAAAATTAAAATGATTCACATGCTTGTAGAA
AAGATGCATCCTCATCTATCCAAACACTATGCATGTGTAGAGTTTTAGAATCTAGATGAAGGTGAGAAAGCACTAAAGCA
CACAGATGGAGGACAAATTGATGGTCAGGAGATCACTGCTACTGCTGTGCTGGCCCCCTAGTCTAGACCACAGCCCTGGC
TATTTAGCTCTCCCAGGAGAATGCCACCACCACCTCCCATGCAGTGCAGGTCTTCTCCATATATGAGG

Alignment

ORF - retro_cpor_363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.26 %
• Parental protein coverage: 88.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDLSGVKKKSLLGVKENNKKSSTRAPSPTKRKDRSDEKSKDRSKDKGTTKESSEKDRGRDKTRKRRSASS
          MDLSGVKKKSLLG.K.NN.KSS.RAPS.TK.KDRSD.KS.D.SKDK..TKESSEKD..R.KT.KR.SASS
Retrocopy MDLSGVKKKSLLGFKDNNEKSSIRAPSSTKCKDRSDDKSMDHSKDKEVTKESSEKDCSRPKTWKRGSASS

Parental  GSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSRSK
          GSSST.S....TSSS..ST..GSSS.SS.S.ASS..GSS..S.SSSSSSSSGS.SPS..R.DNRRRS.SK
Retrocopy GSSSTVS----TSSSNCSTNAGSSSSSSVSLASSCPGSSRISHSSSSSSSSGSSSPSPCRRDNRRRSHSK

Parental  SKPPKRDEKERKRRS-PSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVE
          SKPPKR.EKERKR.S..SPKPTKVHIGRLTRN.T.......FSTYGKIKMI.M.VE.MHPHLSK.YA.VE
Retrocopy SKPPKRGEKERKR*S<LSPKPTKVHIGRLTRNYT----LAVFSTYGKIKMIHMLVEKMHPHLSKHYACVE

Parental  FENPDEAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMR
          F.N.DE.EKALKH.DGGQIDGQEITATAVLAP..RP.P..FS.PRRM.PPPPM..RS.P.MR
Retrocopy F*NLDEGEKALKHTDGGQIDGQEITATAVLAP*SRPQPWLFSSPRRMPPPPPMQCRSSPYMR

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	102.26 RPM
SRP017611_kidney	0.00 RPM	69.83 RPM
SRP017611_liver	0.00 RPM	22.68 RPM
SRP040447_lung	0.00 RPM	77.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	70.05 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_363 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_363 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004866	4 retrocopies	retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Cavia porcellus	ENSCPOG00000002066	2 retrocopies	retro_cpor_363 , retro_cpor_953,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Pan troglodytes	ENSPTRG00000031310	1 retrocopy	retro_ptro_1967,
Pteropus vampyrus	ENSPVAG00000005105	1 retrocopy	retro_pvam_296,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,