RetrogeneDB ID: retro_cpor_1547

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_98:484532..485420(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANGEL2
• Ensembl ID: ENSCPOG00000003875
• Aliases: None
• Description: None

Sequence

>retro_cpor_1547
AGAAAACAGCAAGGCATGACAAAAAGGGAATGGGAATACGCACATAACCGTAATAAAGAAAACGCCAAGATCCCGGGAGA
CAAAAATGATTCCATGTGTGAAGCCAGTGAGAACGAGTTTGATTTTTCAGTGATGTCCTGTAATATACTTTCGTGAGATT
TATTGGAAGATAATTCACACCTTTACAGACACTGCTGACAGCCAGTATGACACTGGAATTTTATGTTTCCCAATACTCGG
AAAGAAATTAAACACTCTGAAGTGCATGTACTTTACCTACCAGAAGGTCAAAAAGATCATTATGGAAAAGAAATCAGGTG
AAGCTTGGAATCACTGGGTTATCACCATGGATATAGGATGTACACAGAAAGGAAACCCAGTGGCTGTGCCATTTGCTTCC
AACGCCCCAGGATTTCACTCTCATCAGCGAACCCAGTGGACTTCTATGCTGTGACAGCCCTCTCTTGGACAAAGACAATA
CTGGATCAGTTTTGGTCTTGCAACCCAAATTGCCCTGCGCTGCGCCTCCTGCAATCTGCGGAGTGAACACACATTTTTGT
AAAATCCGAGACGAGGTGATATCAAGCTGACCCAGCTGGCCATTCTATGGCAGAGACTTCCAGTGTTGCTCACCAGAAAG
ATGATGGCAGTTTCTGTCCCACTGTTACGTGTGGTGACTATAACTCTGTTCTTGATTCTCCACTCTATAGTTTCATGAAG
AAAGGAAGGTTGAATTATGAAGGACCTGCTATAGGAAAGGCAGCTGGCTAAGAACAGTCTTTTTGGGGACAAAGAATTTT
AGCTAGACCTAGTCAGCCCCCAAACCTAGGTATCTCACAGAACTGTGTGTATGAGGCACAGGAGGTCCCAAAAGTAGAAA
AGTCAGGT

Alignment

ORF - retro_cpor_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.43 %
• Parental protein coverage: 54.3 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKHQGMIKRKWEYVCNHNKENAKIQGDENVDPTCEDSEDKFDFSVMSYNILSQDLLEDNSHLYRHCRRPV
          RK.QGM.KR.WEY..N.NKENAKI.GD.N.D..CE.SE..FDFSVMS.NILS.DLLEDNSHLYRHC..PV
Retrocopy RKQQGMTKREWEYAHNRNKENAKIPGDKN-DSMCEASENEFDFSVMSCNILS*DLLEDNSHLYRHC*QPV

Parental  LHWSFRFPNILKEIKHFDADVLCLQEVQEDHYGKEIRPSLESLGYHCEYKMRTGRKPDGCAICFKHSKFS
          .HW.F.FPN..KEIKH....VL.L.E.Q.DHYGKEIR.SLESLGYH..Y.M.T.RKP.GCAICF.....S
Retrocopy *HWNFMFPNTRKEIKHSEVHVLYLPEGQKDHYGKEIR*SLESLGYHHGYRMYTERKPSGCAICFQRPRIS

Parental  LLSVNPVEFYR-RDIPLLDRDNIGLVLLLQPKTACATSPAICVANTH-LLYNPRRGDIKLTQLAML-LAE
          L.S.NPV.FY...D.PLLD.DN.G.VL.LQPK..CA..PAIC..NTH..L.NPRRGDIKLTQLA.L..AE
Retrocopy LSSANPVDFYA<CDSPLLDKDNTGSVLVLQPKLPCAAPPAICGVNTH<FL*NPRRGDIKLTQLAIL<MAE

Parental  ISSVAHQK-DGSFCPIVMCGDFNSVPGSPLYSFIKEGRLNYEGLAIGKVSGQEQSSRGQRILSIPIWPPN
          .SSVAHQK.DGSFCP.V.CGD.NSV..SPLYSF.K.GRLNYEG.AIGK..G.EQS..GQRIL..P..PPN
Retrocopy TSSVAHQKDDGSFCPTVTCGDYNSVLDSPLYSFMKKGRLNYEGPAIGKAAG*EQSFWGQRILARPSQPPN

Parental  LGISQNCVYEAQQGPKVAESG
          LGISQNCVYEAQ..PKV..SG
Retrocopy LGISQNCVYEAQEVPKVEKSG

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	0.35 RPM	15.18 RPM
SRP017611_kidney	0.00 RPM	10.15 RPM
SRP017611_liver	0.00 RPM	7.14 RPM
SRP040447_lung	0.00 RPM	18.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.40 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1547 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1547 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003875	1 retrocopy	retro_cpor_1547 ,
Mus musculus	ENSMUSG00000026634	1 retrocopy	retro_mmus_1690,