RetrogeneDB ID: retro_cpor_873

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_30:2836840..2837167(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM1
• Ensembl ID: ENSCPOG00000008951
• Aliases: None
• Description: None

Sequence

>retro_cpor_873
GCCTTCTACCAGAGCATTTTCAGACTCATGAGGAAATAGCAGGTGGACATCAGGACAGATGCAAAACACCATCAAAGAAA
AACCAGTCCGTGCTAAATGAAACCAGCATGCTGTTTCTGAAAAACAAAAATCTCACAGACACAGAGCTGTGTAGAGATGA
ATGCACAGCCAAGATGAAACAGGGCTGCATTATGAGCTTCTGGACCCAAGACCAATTCATCTGCCTCTTATAAGCCTCAT
CAACTATGAGGTCTGGGACTTTGAATCCTGGAAAAACTGAGGAAACTTTCCAAACCAGTGTATCTCAAGTCTCATGATGA
AATCTCC

Alignment

ORF - retro_cpor_873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.48 %
• Parental protein coverage: 91.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SLYRSIFRLARKWHA-ASGHMEDTIKER-KYILNEARTLFRKNKNLTDTDLIKQCIAECTARI-EIGLHY
          ..Y.SIFRL.RK.....SG.M..TIKE.....LNE...LF.KNKNLTDT.L...C..ECTA...E.GLHY
Retrocopy AFYQSIFRLMRK*QV>TSGQMQNTIKEK>QSVLNETSMLFLKNKNLTDTEL---CRDECTAKM<ETGLHY

Parental  QIPYPRPIHLPPMGLT-PLRGRGFRTQEKLRKLSKPVYLKSHDEIS
          ....PRPIHLP...L...L.G.G....EKLRKLSKPVYLKSHDEIS
Retrocopy ELLDPRPIHLPLISLI<QL*GLGL*ILEKLRKLSKPVYLKSHDEIS

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	0.06 RPM	7.02 RPM
SRP017611_kidney	0.00 RPM	9.11 RPM
SRP017611_liver	0.00 RPM	7.05 RPM
SRP040447_lung	0.00 RPM	6.81 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_873 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_873 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 3 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008951	1 retrocopy	retro_cpor_873 ,
Monodelphis domestica	ENSMODG00000007076	3 retrocopies	retro_mdom_1844, retro_mdom_721, retro_mdom_807,
Sarcophilus harrisii	ENSSHAG00000006127	6 retrocopies	retro_shar_156, retro_shar_270, retro_shar_709, retro_shar_795, retro_shar_798, retro_shar_801,