RetrogeneDB ID: retro_cpor_235

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_105:3131226..3131694(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAF2
• Ensembl ID: ENSCPOG00000006427
• Aliases: None
• Description: None

Sequence

>retro_cpor_235
GAGCAAGACAGTAGAACTATCTCACATCATTTTTGGAAAGTTGAAGGAAGCAGTAAAGTTCACCATAATGTGGAACAACA
GCGGCAGCAACATATACAAAATTCAAGTAAGACTCCCAGTTTTGTAAAGCAGTCTCCACCTGAAGACAAGATGTCCCCAA
CATCTCTAATGGATGGTATTGAAAGAGAACTAAAGGCACAGATGAGCAGCTGTGTTAGCTCGTCAGATTCCACAAGTTCA
TCATCATCAAGTAGTGGGATAGTTCTAGTGACTCAGATGATGAAGAGGGACGATCTTCCTCTACTCCAAGGGATTGTGTG
TCAGGACATCCTACTATGTCCAAATACCTCAGTACAGGATTTCTGATACAGCTGCTGGTCATATCAATTTCATGACAACA
GCAGCATTCTGATGAACACTTTACGTAATGATTTGCAGCTGAGTGACTCAGGAAGTGATAGTGATGAC

Alignment

ORF - retro_cpor_235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKLSSNITVKKTRVEGSTKVHHNMEQQQPQHMRNSSKTPDFAKHSPPEDKMSPTSLMDDIERELKAEASL
          E..S..I......VEGS.KVHHN.EQQ..QH..NSSKTP.F.K.SPPEDKMSPTSLMD.IERELKA..S.
Retrocopy EQDSRTISHHFWKVEGSSKVHHNVEQQRQQHIQNSSKTPSFVKQSPPEDKMSPTSLMDGIERELKAQMS-

Parental  MDQMSSCDSSSDSTSSSS-SSSEDSSSDSDDEEGR-SSTPRSCVSGHPTMS-DISQYRISDTATGH-NRF
          ....SS.DS.S.S.SSS...SS.DS....DDEEGR.SSTPR.CVSGHPTMS..I.QYRISDTA.GH...F
Retrocopy -SCVSSSDSTSSSSSSSG<DSSSDS----DDEEGRSSSTPRDCVSGHPTMS<QIPQYRISDTAAGH<YQF

Parental  PDNSAILMNTLRNDLQLSDSGSDSDD
          .DNS.ILMNTLRNDLQLSDSGSDSDD
Retrocopy HDNSSILMNTLRNDLQLSDSGSDSDD

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	0.17 RPM
SRP017611_kidney	0.00 RPM	3.25 RPM
SRP017611_liver	0.00 RPM	0.09 RPM
SRP040447_lung	0.00 RPM	2.50 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.35 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_235 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_235 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006427	1 retrocopy	retro_cpor_235 ,
Felis catus	ENSFCAG00000018226	1 retrocopy	retro_fcat_1398,
Macropus eugenii	ENSMEUG00000005416	1 retrocopy	retro_meug_1621,
Monodelphis domestica	ENSMODG00000018271	1 retrocopy	retro_mdom_25,
Tupaia belangeri	ENSTBEG00000017542	1 retrocopy	retro_tbel_4110,