RetrogeneDB ID: retro_cpor_1443

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_84:2025704..2026576(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSCPOG00000002914
• Aliases: None
• Description: None

Sequence

>retro_cpor_1443
AGGAAATTCATGAACCCTTTCAATATGCCCAACCTGTATTAGAAGCTAGAGCATGATCCCTGGACAAGGATGCTGCTCAG
TGACCCTATGTACTGGGAGCTGATTGAGCAAATATCTGCTCTGGGCATGCAGCTACAAGACCCTCAGATCATGACCATAC
TCTGTGTCCCGCTTGGGGTTGATCTGGCCAGCATGGATGAGGAGGAAGAGGCTTCAACACTCCTCTTCCTCCTCCTCCCA
AAAAGGAGACCAAGCCAGAGCCCATGGAAGAGGATCTTCCAGAGAATAAGAAGCAAGCACTGAAAGAAAAAGAGTCAGGA
AACGATGCCTACAAGAAGAAAGATTTTGACGCAGCACTGAAGCATTACGACAGAGCCAAGGAGCTGGACCCCACCAACCT
GACTCACATTGCCAATTAAGCAGGGGATACTTTGAAAAGGGCAACTATAATAAATCCTGGGAGCTTCATGAGAAGGCCAT
CAAAGTGGGGAGAGAAAACTGGGAAGACTCTCGACAAATTGCCGAAGCTTATGCTGGAAAGCCGAAGCTTATTACTTCAA
AGAGGAAAAGTACAAGGATGCCATCCATTTCTACAACAAGTCTTTGGCAGAGCAGCAAACCCCAGATGTATTGAAAAAAT
GCCAGCAGGCAGAGAAAATCCTGAAGGAGCGAGAGTGGCTGGCCTATATACACCCTGACTTGGCTTTAGAGGGTAAGAAC
AAGGGCAATAGGTGTTTCCAGAAAGGAGACTATCCTCAGGCCATAAAGCACTATGCAGGAACCATTAAACAGAACCTACC
AGATGCCAAAATGTACAGCATCGAGCTGCCTGCTACACCAAGCTTCTGGAGTTCCAGCTGGCGCGCAGGGAC

Alignment

ORF - retro_cpor_1443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 54.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKFMNPFNMPNLYQKLENDPRTRTLLSDPTYWELIEQLRNKPSDLGTKLQDPRIMTTLSVLLGVDLGSMD
          RKFMNPFNMPNLY.KLE.DP.TR.LLSDP.YWELIEQ.....S.LG..LQDP.IMT.L.V.LGVDL.SMD
Retrocopy RKFMNPFNMPNLY*KLEHDPWTRMLLSDPMYWELIEQI----SALGMQLQDPQIMTILCVPLGVDLASMD

Parental  EEEEAAT-PPPPPPPKKETKPEPMEEDLPENKKQALKEKELGNDAYKKKDFDTALKHYDRAKELDPTNMT
          EEEEA.T..P.PPPPKKETKPEPMEEDLPENKKQALKEKE.GNDAYKKKDFD.ALKHYDRAKELDPTN.T
Retrocopy EEEEAST<TPLPPPPKKETKPEPMEEDLPENKKQALKEKESGNDAYKKKDFDAALKHYDRAKELDPTNLT

Parental  YITNQAA-VYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR-IGNSYFKEE-KYKDAIHFYNKSL
          .I.N.A...YFEKG.YNK..EL.EKAI.VGREN.ED.RQIA.AYA......Y...E.KYKDAIHFYNKSL
Retrocopy HIAN*AG<GYFEKGNYNKSWELHEKAIKVGRENWEDSRQIAEAYAG<KAEAYYFKEEKYKDAIHFYNKSL

Parental  AEHRTPDVLKKCQQAEKILKEQERLAYINPDLALEEKNKGNECFQKGDYPQAMKHYTEAIKRNPRDAKLY
          AE..TPDVLKKCQQAEKILKE.E.LAYI.PDLALE.KNKGN.CFQKGDYPQA.KHY...IK.N..DAK.Y
Retrocopy AEQQTPDVLKKCQQAEKILKEREWLAYIHPDLALEGKNKGNRCFQKGDYPQAIKHYAGTIKQNLPDAKMY

Parental  S-NRAACYTKLLEFQLALKD
          S..RAACYTKLLEFQLA..D
Retrocopy S<HRAACYTKLLEFQLARRD

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	111.12 RPM
SRP017611_kidney	0.00 RPM	101.76 RPM
SRP017611_liver	0.00 RPM	60.68 RPM
SRP040447_lung	0.00 RPM	94.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	105.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1443 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1443 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443 ,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,