RetrogeneDB ID: retro_cpor_1135

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:28112965..28113680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IKZF3
• Ensembl ID: ENSCPOG00000005792
• Aliases: None
• Description: None

Sequence

>retro_cpor_1135
AAAGTTAAGGATGAACGTGGTAAAAAAGAGAAGAATATTGTAAGCCATTGCCCAGGGGAAATGTGCAAGAACCTGACATT
GCTTACAGCTATGCAAGGGAACATAATGCATATGAAACCATTAAGTTGGAGAGCCATCTCTCACATGATAATAACAAGCC
AATCAGTGGGAAGATAAGCTTCCATGCGTGTGAATTATCTTGTATTAGTTTCCATGTCTTAATGGTTTGTAAGTGGAGCC
ATATTGGTGAATGCCCTTTGTGGTGTAATTAGCATGGGGCATTTTTACTCAGAAAGGTAGACTCCTCCACCACAATACAC
TGCACAAAGAAAAAAATACTTTTAAAACCTGTGCATGCCAGTGGAGAGATGCATTCATGGGGCACCTTGGGAATCATTCT
GTGGAGAAGCCCAAAAAATGTGAGTTTGCAGGAGTTACAAGCAGAGAAGTTCCTGTGAGGAGCACATGGAGTACTGTTGC
ACATTTCTTCAGAGCTCTGACGTGCAGGACACAGCAAGAGCGAGACCAAACACATCAGAGCAGAAATGGGAAGTGACAGA
GCTCTGGTTCTGGACAGATTAGCAAGTAATGTGGCAAAACAAAAAAGCCCAATACTTCAGAAATTCATTGGTGAGAAGTG
CCACTGCTTTGGCACCAATTATAATTCCAGCTATGTGCAGGAGAAGGAAGAGAGATAAAACAGACCTGAATGATG

Alignment

ORF - retro_cpor_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.96 %
• Parental protein coverage: 53.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KVKDEYSEREENVL-KPEPLGNMEEPEIPYSYAREYTEYDSIKLERHAAAYDSGRPAGGKMNCDVCGLSC
          KVKDE....E.N...KP.P.GN..EP.I.YSYARE...Y..IKLE.H....D...P..GK.....C.LSC
Retrocopy KVKDERGKKEKNIV<KPLPRGNVQEPDIAYSYAREHNAYETIKLESHLS-HDNNKPISGKISFHACELSC

Parental  ISFNVLMVHKRSHTGERPFQCNQCGAS-FTQKGNLLRHIKLHTGEKPFKCHLCSYACQRRDALTGHLRTH
          ISF.VLMV.K.SH.GE.P..CN..GA..FTQKG.LL.H..LH.....FK......ACQ.RDA..GHL..H
Retrocopy ISFHVLMVCKWSHIGECPLWCN*HGAF<FTQKGRLLHHNTLHKEKNTFK----TCACQWRDAFMGHLGNH

Parental  SVEKPYKCEF-CGRSYKQRSSLEEHKERCRTFLQSPDLGDTASA-EARHIKAEMGSERALVLDRLASNVA
          SVEKP.KCEF.C.RSYKQRSS.EEH.E.C.TFLQS.D..DTA.A.E..HI.AEMGS.RALVLDRLASNVA
Retrocopy SVEKPKKCEF<C-RSYKQRSSCEEHMEYCCTFLQSSDVQDTARA<ETKHIRAEMGSDRALVLDRLASNVA

Parental  KRKSSMPQKFIGEKRHCFDVTYNSSYLYEKDS-EMMQTRMM
          K.KS...QKFIGEK.HCF...YNSSY..EK...E..QT.MM
Retrocopy KQKSPILQKFIGEKCHCFGTNYNSSYVQEKEE<EIKQT*MM

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.42 RPM
SRP017611_liver	0.00 RPM	0.09 RPM
SRP040447_lung	0.00 RPM	4.06 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1135 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1135 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	ENSCPOG00000005792	1 retrocopy	retro_cpor_1135 ,
Cavia porcellus	ENSCPOG00000021914	1 retrocopy	retro_cpor_3,