RetrogeneDB ID: retro_cpor_928

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:20547552..20548286(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD1
• Ensembl ID: ENSCPOG00000011863
• Aliases: None
• Description: None

Sequence

>retro_cpor_928
AATGGGCGGGCTGATTTTTGAGAGCCGAATGCAGAAGTTTCAAGACCAATTCCCCTCACAGGGGCTGATTACATTCCAAC
AGAGGAAGACAGAAGAACGTTTGCAGAACACAAGGATGAAAGCTTCTGGTTCAGATCTGAGCCTCTGGCTGCCTCAAGTA
TGTTGATTACTCATGGACTAATTAGTAAAGGAATTTTTTCAAGTCATCCCAGATTTGGTTCCATCCCTATACTTACATTT
GCTTGTATCATGGGATACTTTGCTGGAAAACTTTCTTATATGAAGACTTGCCAAGTAAAGTTCAAGAATCTCAAAAATTC
CCCTCTTCGACAAGCTTTATGATCAGGACTGCATGACAATCTTCACCACTTGGACCCTATTCTCAAAAGTCAAAATATGC
CTCCAATGTGAGTGGTCAGTCCTCTTTTGTACCCTCCCCTGCAGCAGACAACATACAAAAGGAGACGCTTCCTCATTATG
AGCCAATTCCATTCACTGCTTCTATGAATGAATCCACTCCCACTGGTGTTTCTGATCATACTGCCCAAGGACCTGATCCT
AACCTTGAAGAAAGCCCCAAAAGAAAACACATTACCCATGAGGAATTAAGACAAAAGAACAGAGAGTCATATGAAGTGAC
TTTTACACAAAAGACTGGCCCCTCAGTCCAGTCGATGCAAGAAAGAGTGCAAAAAAAAGTCACAGTAAACAAATATGGAG
ATACTTGGGATGAG

Alignment

ORF - retro_cpor_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.38 %
• Parental protein coverage: 99.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGRADFREPNAEVPRPIPLIGADYIPTEEERRMFAECNDESFWFRSVPLAATSMLITQGLISKGILSSHP
          NGRADF.EPNAEV.RPIPL.GADYIPTEE.RR.FAE..DESFWFRS.PLAA.SMLIT.GLISKGI.SSHP
Retrocopy NGRADF*EPNAEVSRPIPLTGADYIPTEEDRRTFAEHKDESFWFRSEPLAASSMLITHGLISKGIFSSHP

Parental  RFGSIPKLIFACIMGYFAGKLSYVRTCQEKFKNLENSPLGEALRSG-QARRSSPSGHYSQKSKYDSNVSG
          RFGSIP.L.FACIMGYFAGKLSY..TCQ.KFKNL.NSPL..AL.SG..A..SSP.G.YSQKSKY.SNVSG
Retrocopy RFGSIPILTFACIMGYFAGKLSYMKTCQVKFKNLKNSPLRQAL*SG<TA*QSSPLGPYSQKSKYASNVSG

Parental  QSSFVTSPAADNIEKEMLPHYEPIPFSASVNESAPTGISDHIAQGPDPNLEESPKRKNITYEELRQKNRE
          QSSFV.SPAADNI.KE.LPHYEPIPF.AS.NES.PTG.SDH.AQGPDPNLEESPKRK.IT.EELRQKNRE
Retrocopy QSSFVPSPAADNIQKETLPHYEPIPFTASMNESTPTGVSDHTAQGPDPNLEESPKRKHITHEELRQKNRE

Parental  SYEVTLTQKTGPSVRPMQETVPKKEVKVNKYGDTWDE
          SYEVT.TQKTGPSV..MQE.V....V.VNKYGDTWDE
Retrocopy SYEVTFTQKTGPSVQSMQERV-XXXVTVNKYGDTWDE

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	231.22 RPM
SRP017611_kidney	0.00 RPM	62.71 RPM
SRP017611_liver	0.00 RPM	62.64 RPM
SRP040447_lung	0.00 RPM	29.76 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_928 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_928 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011863	1 retrocopy	retro_cpor_928 ,
Echinops telfairi	ENSETEG00000005961	1 retrocopy	retro_etel_1731,
Latimeria chalumnae	ENSLACG00000014002	1 retrocopy	retro_lcha_88,
Macropus eugenii	ENSMEUG00000010655	2 retrocopies	retro_meug_1692, retro_meug_2016,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103,
Sarcophilus harrisii	ENSSHAG00000018132	1 retrocopy	retro_shar_74,
Ictidomys tridecemlineatus	ENSSTOG00000014963	1 retrocopy	retro_itri_986,