RetrogeneDB ID: retro_cpor_1274

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_62:1191620..1192394(-)
• 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_1274
AAGCATGGAAATAACCAGCCTGCAAGAACTGGCACACTGTCGAGAACAAATCCTCCTACTCAGAAACCACCAAGTCAGAA
ACCACCTCCCATGTCAGGCCGGGGAGCATTGGGGCGAAATACTCCTTACAAAATCCTGGAGCCTGTTAAACTCCCAATAG
TCCCTAATGATTACATGACCAGTCCTGCAAGACTTGGAGGTCAGCATAGTCCAGGCAGGAGAGCTTCTTTAAATCAGAGA
CCAAGGACACACAGTGGAAGCAGTGGAGGAGAAGGAGCCGAGAGGACAGTGGGAGCAGTAGTATTGGCATTCCCACTGCT
GTACCTAAGCCTTCCCCATCCACTACTGATCAGCTGCCCCGGGCTCGGCTCCTGGTTCCCAGTACGGCACAATGACCAGG
CAGATTTCTCAATACAACTCTACCACTTCCTCGACATCTTCTGGAGGATACAGACAAACTCCCTCTGTGACTGCTCAGTT
TTCTGCTCAGCCTCATGTTAATGGAGGTCCACTTTACGCCCAAAATTCAATTTCTATTGCTCGCTCCTTCCCCCGATGCC
TCAATTGACTCCACAGATACCTCGCACAGGCTTCGTGGCCAGGGTGCAGAAAAATATTGCTGACAGCCCAACTCCACCGT
CACCACCTCCACCAGATGACATTCCCGTATTTGCTGACTCTCCACCTCCCCCGCCTCCTCCCCCAGTGGACTGTGAAGAT
GAGGGAGCTGCAGTAGTCCAGGATAATGACCCATATGCAGATGGGAATCCTGCC

Alignment

ORF - retro_cpor_1274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KHGNNQPARTGTLSRTNPPTQKPPS---PPMSGRGTLGRNTPYKTLEPVKPPTVPNDYMTSPARLGSQHS
          KHGNNQPARTGTLSRTNPPTQKPPS...PPMSGRG.LGRNTPYK.LEPVK.P.VPNDYMTSPARLG.QHS
Retrocopy KHGNNQPARTGTLSRTNPPTQKPPSQKPPPMSGRGALGRNTPYKILEPVKLPIVPNDYMTSPARLGGQHS

Parental  PGRTASLNQRPRTHSGSSGGSG-SRENSGSSSIGIPIAVPTPSPPTIA-PAAPGSAPGSQYGTMTRQISR
          PGR.ASLNQRPRTHSGSSGG.G.SRE.SGSSSIGIP.AVP.PSP.T....AAPGSAPGSQYGTMTRQIS.
Retrocopy PGRRASLNQRPRTHSGSSGGEG<SREDSGSSSIGIPTAVPKPSPSTTD<SAAPGSAPGSQYGTMTRQISQ

Parental  HNSTTSSTSSGGYRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPPPP-PMPQLTPQIPLTGFVARVQENI
          .NSTTSSTSSGGYR.TPSVTAQFSAQPHVNGGPLY.QNSISIA...P.PMPQLTPQIP.TGFVARVQ.NI
Retrocopy YNSTTSSTSSGGYRQTPSVTAQFSAQPHVNGGPLYAQNSISIARSFP<PMPQLTPQIPRTGFVARVQKNI

Parental  ADSPTPPPPPPPDDIPIFDDSPPPPPPPPVDYEDEEAAVVQYNDPYADGDPA
          ADSPTPP.PPPPDDIP.F.DSPPPPPPPPVD.EDE.AAVVQ.NDPYADG.PA
Retrocopy ADSPTPPSPPPPDDIPVFADSPPPPPPPPVDCEDEGAAVVQDNDPYADGNPA

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	0.17 RPM	35.49 RPM
SRP017611_kidney	0.10 RPM	30.25 RPM
SRP017611_liver	0.00 RPM	23.85 RPM
SRP040447_lung	0.08 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_1274 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1274 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,