RetrogeneDB ID: retro_cpor_996

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_39:5812297..5813380(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000013736
• Aliases: None
• Description: Nucleolar GTP-binding protein 1 [Source:UniProtKB/TrEMBL;Acc:H0VPF1]

Sequence

>retro_cpor_996
ATGAAAGGGGAATTAGAGCTCTTCCAGAATATCAGACCCCTCTTTATCAACAAACTCTTACAGTTGCAGCAAACAAATGT
GATGTGAAGAGAATAGCTGAACTTCCTAAATATGATCTGGAAATATTTATAGACTTACAGTCCGAAGGGTTCTCTGGTTA
AAGAAATTAGCACCCTGGCTGAGAAAGGTGTTATTAAAGTTAAAACAGAGACTTGTGATGGGCTTTTGGCTCATTGAGTA
GAAACCAAAATGAAAGGAAATGAAGTGAATGAATGCTAAATGGATTGCACTTAGCTATTCCAAACAAGAGAGATGATAAG
GAGAGGCAACCCTCCATCCCAGAAGGAGTGGTGGCATGCAACAAGAGAATGGAAATTGGGGAACACAAGAAAAGGGAATG
AGGTCTTGAGCTGGAAGTGGGAGATATTTTGGATCGTTGAAAATACTGGGATTTAATGAATTCATCTGAAAAATATGAGA
AGATACCAGAGATCTGGGAAAGTCAATGTAGCTGTTTATACTGACCCTGCTATCATGAAGAAATTGAAAGAATTAGAAAA
AGAAAAATTAAGAACAGCTATGAAAGTATGACAGTAAGTCTGAAAGTGAAGATGAAGAAATGACGGAAATCTGACAGCTG
GCAAAACAGATTAGAGAAAAAAAGAAATTGAAAATTCTGTAATCAGAAGAAATGAATACCCAGGGATCAAGGATGCCTAA
GATTCAGTAGACAATTTTGGACAATTAGATGTAAAGTCTTGATATTGACATGAATGATAAAAACAATGCCCAGTATGCAA
TCCAGGCAACTTGGTCTCAGAGTGTCGCTAGGAAAAGAAAGCGAGAAGGTTCTGTTCCACCCACTTCTGTAGCCCAGAGT
TAGAGTTGCTCTCAAACTCTATTCAACGTTTCTGGTCTTTGGGATGTGAAGATGGTGAAGAAATCCAAGATTATAAAAAA
GAATGCTCAGAAGAAGATGAATCGCTTGGGGAAGAAAGAGGAGGCAGTTATACATATATTTGGTATGAAAGCCAAACACT
TAACCCTCTGGAAAGAGGAAAGCTCTGTAAAAAGGACAGAAGA

Alignment

ORF - retro_cpor_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.53 %
• Parental protein coverage: 58.36 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LKEQLELFQNIRPLFVNK-PLIVVANKCDVKRIAELPEDDQKIFIDLQAEGFP-VIETSTLTEEGVIKVK
          .K..LELFQNIRPLF.NK..L.V.ANKCDVKRIAELP..D..IFIDLQ.EGF..V.E.STL.E.GVIKVK
Retrocopy MKGELELFQNIRPLFINK<TLTVAANKCDVKRIAELPKYDLEIFIDLQSEGFS>VKEISTLAEKGVIKVK

Parental  TEACDRLLAHRVETKMKGNKVNE-VLNRLHLAIPNKRDDKERPPFIPEGVVARKKRMDIGEPKKKRERDL
          TE.CD.LLAH.VETKMKGN.VNE..LN.LHLAIPNKRDDKER.P.IPEGVVA..KRM.IGE..KKRE..L
Retrocopy TETCDGLLAH*VETKMKGNEVNE<MLNGLHLAIPNKRDDKERQPSIPEGVVACNKRMEIGE-HKKRE*GL

Parental  ELEMGDDYILDLQKYWDLMNSSEKYDKIPEIWEGHNVADYIDPAIMKKLEELEKEEELRTAAGEYDSESE
          ELE.GD..ILD..KYWDLMNSSEKY.KIPEIWE......Y..P......E...K....R.....Y.S...
Retrocopy ELEVGD--ILDR*KYWDLMNSSEKYEKIPEIWESQCSCLY-*PCYHEEIERIRK----RKIKNSYESMTV

Parental  S-EDEEMLEIRELARQIREKKKLKILQ---SKEKNTQGPRMPRTAKKVQRTVLENEMRSLGIDMDDKDNT
          S....E..E..E...........K.L....S.E.NTQG.RMP......Q.T.L.N.M.SL.IDM.DK.N.
Retrocopy S<SESEDEEMTEI*QLAKQIREKKKLKIL*SEEMNTQGSRMPK----IQ*TILDN*M*SLDIDMNDKNNA

Parental  HYAIQARRSRSITRKRKREDSVPPTSVARSRSCSRTPRDVSGLRDMKMVKKAKTMMKNAQKKMNRLGKKG
          .YAIQA..S.S..RKRKRE.SVPPTSVA.S.SCS.T...VSGL.D.KMVKK.K...KNAQKKMNRLGKK.
Retrocopy QYAIQATWSQSVARKRKREGSVPPTSVAQS*SCSQTLFNVSGLWDVKMVKKSKIIKKNAQKKMNRLGKKE

Parental  EADRHVFDMKPKHLL-SGKRKA-GKKDRR
          EA..H.F.MK.KHL..SGKRKA..KKDRR
Retrocopy EAVIHIFGMKAKHLT>SGKRKA>CKKDRR

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	22.95 RPM
SRP017611_kidney	0.00 RPM	39.89 RPM
SRP017611_liver	0.00 RPM	22.37 RPM
SRP040447_lung	0.00 RPM	29.66 RPM
SRP040447_skeletal_muscle	0.01 RPM	24.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_996 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_996 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008494	2 retrocopies	retro_cjac_2592, retro_cjac_992,
Cavia porcellus	ENSCPOG00000013736	1 retrocopy	retro_cpor_996 ,
Rattus norvegicus	ENSRNOG00000016217	2 retrocopies	retro_rnor_1961, retro_rnor_2882,
Sarcophilus harrisii	ENSSHAG00000014713	1 retrocopy	retro_shar_654,
Ictidomys tridecemlineatus	ENSSTOG00000010042	1 retrocopy	retro_itri_1466,