RetrogeneDB ID: retro_cpor_1375

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_76:7851012..7851975(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABI1
• Ensembl ID: ENSCPOG00000014424
• Aliases: None
• Description: None

Sequence

>retro_cpor_1375
AAGCATGGAAATAACCAACCTGCAGGAACCAGCACATAATGGAGCACAAATACTCCTGCTCAGAAACAACCAAACCCTCC
CATACATGGCTGGGGAACACTGGAGAGGAGTCCTCCTATGAAACCTTGCAGTCTGCTAAATGTCCACCAGTCCCTAATGA
CTTCATGTCCAGTCCTGCAAGGCTTAGAAGTCAGCATAGTCCAGGCAGGACAGCTTCTTAAATCAGAGACCAAAGACACA
CAGTGGAATTAGTGGAGGAAGGGAAGTCGAAAGAACAGAAGGCTCAGTGGTATAGGCATCCCCACTGCTACACCTGCTCC
CTCCCCACTCAGGATGGGACCAGTGGTCCAGGTCTTGGCTGCTGGTTCCAGTAGGGCACCAGGATCAGTCAGATTTCTCC
ACACCACTCTGTCACGTCCTCCACAGCTTCTGGTGGGTATAAATGAATTCCCTCTGTGACTGCTCAGTTTTCTTCCATGC
TGCAAGTTATTGGAGGTCCACTTCATTCTCAGAATTCAGTTTCTATTGCTCCACCCCTCCCACCACATGTCCATTGACTC
CATAGATACTTTGTCCAGGCTTCATGGCCAGGGTGCAGGAAAACATTGCTGACAGCCCAACTCCACCACCTCCATCTCCA
CCAAATCGTGTTCTCATATCTGATGACTCTACTGCACCTCTCCTGCCCTTCCCCTAGGCACTATAACATGAGAAAGCTGG
AGCAGCTCAGTATAATGATCCCTATGCAGTTGAGGATCCTACCTGGGCCCCCAAGAATTATATTGAGAATACTGTTACAA
TATATGATTGTAAAAAAGACAAAGCTGATGAGCTGTCATTTATAGAGGGTGCAGTAATTGATTTTAGAAATAAGAACAAT
GATGGCTAGCAGGAAGAGGTCTGCAGTCCAGTGACTGGTCACTTCCTGGGATCTGTGTTGAATCAGGCATGCACTATACT
GAT

Alignment

ORF - retro_cpor_1375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.61 %
• Parental protein coverage: 67.15 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KHGNNQPARTGTLSRTNPPTQKPPSPPMSGRGTLGRNTP-YKTLEPVKPPTVPNDYMTSPARLGSQHSPG
          KHGNNQPA.T.T...TN.P.QK.P.PP..G.GTL.R..P.Y.TL...K.P.VPND.M.SPARL.SQHSPG
Retrocopy KHGNNQPAGTST*WSTNTPAQKQPNPPIHGWGTLERSPP<YETLQSAKCPPVPNDFMSSPARLRSQHSPG

Parental  RTAS-LNQRPRTHSGSSGG-SGSRENSGSSSIGIPIAVPTPSPPTIAPAAPGSAPGS-QYGTMTRQISRH
          RTAS.LNQRP.THSG.SGG..GSR.N...S.IGIP.A.P.PSP....P.....A.GS.Q.GT...QIS.H
Retrocopy RTAS<LNQRPKTHSGISGG<KGSRKNRRLSGIGIPTATPAPSPLRMGPVVQVLAAGS<Q*GTRISQISPH

Parental  NSTTSSTSSGGYRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPP-PPPMPQLTPQIPLTGFVARVQENIA
          .S.TSST.SGGY...PSVTAQFS....V.GGPL.SQNS.SIAPP.PP....LTP.I...GF.ARVQENIA
Retrocopy HSVTSSTASGGYK*IPSVTAQFSSMLQVIGGPLHSQNSVSIAPP<PPTTCPLTP*ILCPGFMARVQENIA

Parental  DSPTPPPPPPPDDIPIFDDSPPPPPPPPVDYEDEEAAVVQYNDPYADGDPAWAPKNYIEKVVAIYDYTKD
          DSPTPPPP.PP....I.DDS..P..P.P.....E.A...QYNDPYA..DP.WAPKNYIE..V.IYD..KD
Retrocopy DSPTPPPPSPPNRVLISDDSTAPLLPFP*AL*HEKAGAAQYNDPYAVEDPTWAPKNYIENTVTIYDCKKD

Parental  KDDELSFMEGAIIYVIKKNDDGWYEGVCNRVTGLF-PGNYVESIMHYTD
          K.DELSF.EGA.I....KN.DG..E.VC..VTG.F.PG..VES.MHYTD
Retrocopy KADELSFIEGAVIDFRNKNNDG*QEEVCSPVTGHF<PGICVESGMHYTD

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	35.49 RPM
SRP017611_kidney	0.00 RPM	30.25 RPM
SRP017611_liver	0.00 RPM	23.85 RPM
SRP040447_lung	0.00 RPM	47.16 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.59 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1375 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1375 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014424	3 retrocopies	retro_cpor_1274, retro_cpor_1375 , retro_cpor_1451,