RetrogeneDB ID: retro_cpor_1308

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_68:7488885..7490112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000022216
• Aliases: None
• Description: None

Sequence

>retro_cpor_1308
TCAGATCTTACAAAGTCCTCAAGGCCAGAAGCTTCAGCAGTTTTAATACAGACTTTACAGATACAACAGCAGAAGCCCCA
GCCTTCCACCCCGCAGGCCCTGGATGCTGGTCTTGTGGTTCAGTTGCAGGCTCTCGCTGCATAGCTTACAGCTGCAGCTG
CAGCAGCCAACACACTTACTCCCTTAGAACAGGGAGTCTCTTTTAACAAGAAGTTGATGGATAGGTTTGATTTTGGTGAA
GATTCTGAGCATAGTGAAGAACCCAAAAAGGAAATTCCAGCTCCTCGACTTTCTCATGTTTCAGAATCTGTGAACAATTC
CATTTTTCTTCAGATAGCGGAACAACTACAACAGCAAAATCTTGAACATCTCAGACAGCAGCTTCTGGAACAGCAACAAC
CACAGAAGGCAACTCCTCAGGATAGTCAAGAAGGAACATTTGGGTCTGAGCATTCGGCGTCACCATCACAAGGGAGTAGT
CAGCAACGTTTTCTTGAACCTGAGGCAACTTTGGATGATTCCATAGATATTCAACAACAGGATATGGATATAGATGAAGG
GCAAGATGGAATACAAGAGGAAGTCTTTGAACAAGAAGCTAAGAAAGTAGCAGTTCGTTCAAGATCAAGGACTCATTCAC
GATCTCGTTCAAAATCACCAAGAAAATAAAGATCCAGGTCACAATCTGGTTCTAGAAAGCGTAAGCACAGAAAGCGATCA
CGCTCCCACTCAAGAGAAAGAAAGAGGAAGTCATACTCAAGTGAAAGGAGAGCCAGAGAAAGGGAGAAAGAACGGCAGAA
AAAGGGGTTACCTCCAATTAGATCTAAAACATTAAGTGTGTGTAGTACTACTCTCTGGGTTGGTCAACTGGACAAGAAGG
CAACACAACAAGATTTAACTAACCTTTTTGAAGAATTTGGACAGATTGAATCTATTAATATGATTCCTCCCAGGGGCTGT
GCTTATGTCTGTATGGTTCATCGGCAAGATGCATTTCGGGCTCTTCAGAAACTCAGTTCTGGATCATACAAAATTGGTTC
CAAGGTCATTAAGATTGTGTGGGCTTTAAACAAGGGTGTAAAAACAGAGTACAAACAATTTTGGGACTTGGATCTTGGAG
TAAGTTACATACCATGGGAAAAAGTGAAAGTGGATGACTTGGATGGTTTTGCAGAAGGAGGCATGATTGATCAGGAAGCT
GTAAATACTGAATGGGAAACTGTAAAA

Alignment

ORF - retro_cpor_1308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.77 %
• Parental protein coverage: 67.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQILQSPQGQQLQQLIQTLQIQQQKPQPSILQALDAGLVVQLQALTAQLTAAAAAANTLTPLEQGVSFNK
          .....S........LIQTLQIQQQKPQPS..QALDAGLVVQLQAL.A.LTAAAAAANTLTPLEQGVSFNK
Retrocopy SDLTKSSRPEASAVLIQTLQIQQQKPQPSTPQALDAGLVVQLQALAA*LTAAAAAANTLTPLEQGVSFNK

Parental  KLMDRFDFGEDSEHSEEPKKEIPAPQLSHVSESVNNSIFHQIAEQLQQQNLEHLRQQLLEQQQPQKATPQ
          KLMDRFDFGEDSEHSEEPKKEIPAP.LSHVSESVNNSIF.QIAEQLQQQNLEHLRQQLLEQQQPQKATPQ
Retrocopy KLMDRFDFGEDSEHSEEPKKEIPAPRLSHVSESVNNSIFLQIAEQLQQQNLEHLRQQLLEQQQPQKATPQ

Parental  DSQEGTFGSEHSASPSQGSSQQHFLEPEATLDDSIDIQQQDMDIDEGQDGVQEEVFEQEAKKVAVRSRSR
          DSQEGTFGSEHSASPSQGSSQQ.FLEPEATLDDSIDIQQQDMDIDEGQDG.QEEVFEQEAKKVAVRSRSR
Retrocopy DSQEGTFGSEHSASPSQGSSQQRFLEPEATLDDSIDIQQQDMDIDEGQDGIQEEVFEQEAKKVAVRSRSR

Parental  THSRSRSRRSPRKRRSRSRSGSRKRKHRKRSRSRSRERKRKSSRSYSSERRAREREKERQKKGLPPIRSK
          THSRSRS..SPRK.RSRS.SGSRKRKHRKRSRS.SRERKRKS...YSSERRAREREKERQKKGLPPIRSK
Retrocopy THSRSRS-KSPRK*RSRSQSGSRKRKHRKRSRSHSRERKRKS---YSSERRAREREKERQKKGLPPIRSK

Parental  TLSVCSTTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAFRALQKLSSGSYKIG
          TLSVCSTTLWVGQ.DKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAFRALQKLSSGSYKIG
Retrocopy TLSVCSTTLWVGQLDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAFRALQKLSSGSYKIG

Parental  SKVIKIAWALNKGVKTEYKQFWDVDLGVTYIPWEKVKVDDLDGFAEGGMIDQETVNTEWETVK
          SKVIKI.WALNKGVKTEYKQFWD.DLGV.YIPWEKVKVDDLDGFAEGGMIDQE.VNTEWETVK
Retrocopy SKVIKIVWALNKGVKTEYKQFWDLDLGVSYIPWEKVKVDDLDGFAEGGMIDQEAVNTEWETVK

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	0.75 RPM	20.99 RPM
SRP017611_kidney	0.52 RPM	15.28 RPM
SRP017611_liver	0.30 RPM	10.53 RPM
SRP040447_lung	0.61 RPM	17.15 RPM
SRP040447_skeletal_muscle	0.34 RPM	10.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1308 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1308 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	ENSCPOG00000022216	1 retrocopy	retro_cpor_1308 ,