RetrogeneDB ID: retro_cpor_593

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:8114812..8115898(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LTV1
• Ensembl ID: ENSCPOG00000013716
• Aliases: None
• Description: None

Sequence

>retro_cpor_593
ATCTTTGCATCAGAGTTTGAGGAAGATGTTGGATTGTTAAATAAAGCAGCTCCAATTTCAGGCCCTCGACTAGATTTTGA
TCCTGACATTGTTGCTGCTCTTCATGATGATTTAGACTTTGATGATCCAGAGAACATGCTTGAAGATGACTTTATTCTTC
AGGCCAATAGGCCAACAGAAAAGGAAGGAGGGATGGATATTCTGAAACCTGAGGGTGAAGACAGCAGTGAGTGGGAAGAT
GAGGATGAGACCGGGAGTGGCAGTGACTCTGCAGATGACCATGACTCTGCAGGCCCGTTGTCAGATGAAGATGTGCCATC
CTTCTTTGGAGATGCTCACAGGCCCATAGAAAAGCATTTGTTCTGGGAGGAGGAAACAAAAAGTCGCTTCACAGAGTATT
CTATGACTTCCTCAGTCATGAGGAGAAATGAGCAGCTGACCCTACATGACGAGAGATTTGAGAAGCTTTATGAACAGTAT
GATGATGAAATTGGAGCTCTGGATAATGCTGAATTGGAAGGTTCCATTCAAGTAGACAGCAATCACTTACAAGAAGTTTT
GAATGACTACTATAAAGAGAAGGCTGAGGATTGTATAAAATTGAATATTCTTGAAACTTTTGAGGATCAAGACCTGCCAG
TGGATGAGCTTGAAGAATCTGAAGAGATGATTACTGTATTTCTTGAAGAAACCAAAGAGAAGTGGGATTGCGGATCCATT
TGCAGTACATACTCCAATTTATACAATCATCCACAGCTTATCAAATACCAACCAAAGCCCAAACAAATCCACTTATCTTC
TAAAACAGGAATACCTCTCAATGTCTTACCTAAGAAAGGACTCAGAGCAAAGTAAGTTGAACGAATGCAGATGATTAATG
GCAGTGATCTGCCCTGGGTATCAACTCATCCATGTTCAAAACATGAAAGCAAAGAGGGTAAAAGAGCAAGAAAGCAAGCT
ATAAAAGAGGAGCGCAAGGAACGAAGAATGGAGAAGAAAGCTGACAAATTAGCGTTCAAACTGGAGAAGAGAAGACAGGA
AAAGGAGCTGCTGAATTTGAAGAAGAACATGGAAGGTCTAAAGCTG

Alignment

ORF - retro_cpor_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.13 %
• Parental protein coverage: 76.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFASEFEEDVGLLNKAAPVSVGPRLDFDPDIVAALDDDFDFDDPENMLEDDFILQANRPTEKEEGMDIPK
          .FASEFEEDVGLLNKAAP.S.GPRLDFDPDIVAAL.DD.DFDDPENMLEDDFILQANRPTEKE.GMDI.K
Retrocopy IFASEFEEDVGLLNKAAPIS-GPRLDFDPDIVAALHDDLDFDDPENMLEDDFILQANRPTEKEGGMDILK

Parental  SEGEDSSEWEDEDETGSGSDSAGDHNSAGPLSDEDVPSFFGDAHRPIEKHLFWEEETKSRFTEYSMTSSV
          .EGEDSSEWEDEDETGSGSDSA.DH.SAGPLSDEDVPSFFGDAHRPIEKHLFWEEETKSRFTEYSMTSSV
Retrocopy PEGEDSSEWEDEDETGSGSDSADDHDSAGPLSDEDVPSFFGDAHRPIEKHLFWEEETKSRFTEYSMTSSV

Parental  MRRNEQLTLHDERFEKFYEQYDDDEIGALDNAELEGSIQVDSNRLQEVLNDYYKEKAENCIKLNTLEPFE
          MRRNEQLTLHDERFEK.YEQYDD.EIGALDNAELEGSIQVDSN.LQEVLNDYYKEKAE.CIKLN.LE.FE
Retrocopy MRRNEQLTLHDERFEKLYEQYDD-EIGALDNAELEGSIQVDSNHLQEVLNDYYKEKAEDCIKLNILETFE

Parental  DQDLPVDELEESEEMITVVLEETKEKWDCESICSTYSNLYNHPQLIKYQPKPKQIHLSSKTGIPLNVLPK
          DQDLPVDELEESEEMITV.LEETKEKWDC.SICSTYSNLYNHPQLIKYQPKPKQIHLSSKTGIPLNVLPK
Retrocopy DQDLPVDELEESEEMITVFLEETKEKWDCGSICSTYSNLYNHPQLIKYQPKPKQIHLSSKTGIPLNVLPK

Parental  KGLTAKQVERMQMINGSDLPRVSTQPRSKHESKEGKRARKQAIKEERKERRMEKKANKLAFKLEKRRQEK
          KGL.AK.VERMQMINGSDLP.VST.P.SKHESKEGKRARKQAIKEERKERRMEKKA.KLAFKLEKRRQEK
Retrocopy KGLRAK*VERMQMINGSDLPWVSTHPCSKHESKEGKRARKQAIKEERKERRMEKKADKLAFKLEKRRQEK

Parental  ELLNLKKNVEGLKL
          ELLNLKKN.EGLKL
Retrocopy ELLNLKKNMEGLKL

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	0.12 RPM	16.62 RPM
SRP017611_kidney	0.00 RPM	20.73 RPM
SRP017611_liver	0.04 RPM	15.45 RPM
SRP040447_lung	0.05 RPM	29.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.79 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_593 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_593 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013716	1 retrocopy	retro_cpor_593 ,