RetrogeneDB ID: retro_cpor_753

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:19984300..19984900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP2
• Ensembl ID: ENSCPOG00000014687
• Aliases: None
• Description: None

Sequence

>retro_cpor_753
AAAGTCTCTGTGGAGCATGCCAGAGCGACAGGAGGTGAAACCATCCCACTGGGTGACCATGGCAGCAGAAACTCAGGTGA
AAGGGATGCTTCAGCTATGACATCACCAACAAGGGAAGCTGAGAGTGCTGAGTGCTGAGGCAACCTGCTTGCACTAAAGC
CAGATCTCAAGCCAAGCATGATGCACCATCACAATGCAGGAACTGGCTGCTACCAGGTGCATCACAATGAAAAGGACAAT
TCAGAATCATGTGCTGTAGAGCAGTCATTTACTTCAGACTCAACACCACAGGTTGTGCAGACTGCTTTTCCAGCACCAGC
ACTAGAATGTGTTACTTCTCCACCTTAAAGTAATATTGTGGAAATATCTACAACTTCAGACACAGAAGTTTATAGTGAGT
TTCATCCTGTGCCACCTCGGTACAGTGTTGCTAACTCTCTTCCAAGAAATGGTGAAGCTGAGAAAGCTAATGCTGCTGCA
ATGGGAGCTATAGCTGCAGAAACATCTATAAGAAATCAGGGGAAAAAGTGTTCCCTAAAAAATGCCTTCAGTGACACAGA
CCAGATTATAGTGGGCAACAATGGCATTTTCATGCTGGCA

Alignment

ORF - retro_cpor_753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.88 %
• Parental protein coverage: 84.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVSAEPAGATGSEAAPPGDRGGRNRGGRGAAAPTSPAGEAEVVEGRGVLPALDRD--PSTMDHHQPGTGR
          .VS.E.A.ATG.E..P.GD.G.RN.G.R.A.A.TSP..EAE..E..G.L.AL..D..PS.M.HH..GTG.
Retrocopy KVSVEHARATGGETIPLGDHGSRNSGERDASAMTSPTREAESAEC*GNLLALKPDLKPSMMHHHNAGTGC

Parental  YQVLHNEEDNSESPATEQPSTSNSTPQVVQVASSTPALETDTSPPPYSSINMEVPTTSDTEVYSEFYPVP
          YQV.HNE.DNSES.A.EQ..TS.STPQVVQ.A...PALE..TSPP.......E..TTSDTEVYSEF.PVP
Retrocopy YQVHHNEKDNSESCAVEQSFTSDSTPQVVQTAFPAPALECVTSPP*SNIV--EISTTSDTEVYSEFHPVP

Parental  PPYSVATSLPTYDEAEKAKAAAIAAAAAETSQRNQEEECPPRDDFSDADQLRVGNDGIFMLA
          P.YSVA.SLP...EAEKA.AAA..A.AAETS.RNQ...C.....FSD.DQ..VGN.GIFMLA
Retrocopy PRYSVANSLPRNGEAEKANAAAMGAIAAETSIRNQGKKCSLKNAFSDTDQIIVGNNGIFMLA

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	16.56 RPM
SRP017611_kidney	0.00 RPM	16.65 RPM
SRP017611_liver	0.00 RPM	13.36 RPM
SRP040447_lung	0.00 RPM	19.95 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_753 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_753 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021282	2 retrocopies	retro_cjac_2643, retro_cjac_2644,
Cavia porcellus	ENSCPOG00000014687	1 retrocopy	retro_cpor_753 ,
Loxodonta africana	ENSLAFG00000000864	1 retrocopy	retro_lafr_841,
Monodelphis domestica	ENSMODG00000001586	2 retrocopies	retro_mdom_1600, retro_mdom_48,
Mustela putorius furo	ENSMPUG00000003366	1 retrocopy	retro_mputfur_1079,
Tupaia belangeri	ENSTBEG00000005780	1 retrocopy	retro_tbel_3231,