RetrogeneDB ID: retro_cpor_748

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:21388136..21388518(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOCS2
• Ensembl ID: ENSCPOG00000015752
• Aliases: None
• Description: None

Sequence

>retro_cpor_748
GCTGAGAAATTTTTGGTATATGAAGTCTCACATTTGGTGATTCTCCAATGTGTGGTGCAGTGTCCTTATTTTTAGGGACT
ACAGGAAATAATTTTAAAGGGAAAAAAGTCATTACTTTAGAATATGAAGTATATATATCAATGGCAGAAAATGAAATCAA
AAAAATCTGTAGTGACATTAGGTAGAAATGGCCTGTAAAACACATAGCAGTGTTCCACAGAGTTGGCTTAGTTCCAGTAT
CAGAAGTAAACATAGTTATTGCTGTGTCCTCATTCCACAGGTATGCATTCCTAGCAGTTGTGAGTTATGCCATTGACATT
TTAAAAGCCAAAGTGCCATATGGAAAAAAATATATGAAGAAACTTTATCATCATGGGAAAAA

Alignment

ORF - retro_cpor_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.86 %
• Parental protein coverage: 92.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AEKLSVDEISQLVI-SPLCGAVSLFVGTTRNNFEGKKVISLEYEAYIPMAENEIRKICSDIRQKWPVKHI
          AEK..V.E.S.LVI.SP.CGAVSLF.GTT.NNF.GKKVI.LEYE.YI.MAENEI.KICSDIR.KWPVKHI
Retrocopy AEKFLVYEVSHLVI<SPMCGAVSLFLGTTGNNFKGKKVITLEYEVYISMAENEIKKICSDIR*KWPVKHI

Parental  AVFHRLGLVPVSEASIVIAVSSAHRAASLAAVSYAIDTLKAKVP-IWKKEIYEESSSSWKR
          AVFHR.GLVPVSE..IVIAVSS.HR.A.LA.VSYAID.LKAKVP.IWKK.IYEE..SSW..
Retrocopy AVFHRVGLVPVSEVNIVIAVSSFHRYAFLAVVSYAIDILKAKVP<IWKK-IYEETLSSWEK

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	3.97 RPM
SRP017611_kidney	0.00 RPM	8.37 RPM
SRP017611_liver	0.00 RPM	10.40 RPM
SRP040447_lung	0.00 RPM	5.40 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.86 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_748 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_748 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005380	1 retrocopy	retro_btau_487,
Cavia porcellus	ENSCPOG00000015752	2 retrocopies	retro_cpor_746, retro_cpor_748 ,
Macaca mulatta	ENSMMUG00000020449	1 retrocopy	retro_mmul_581,
Monodelphis domestica	ENSMODG00000019459	1 retrocopy	retro_mdom_1654,
Oryctolagus cuniculus	ENSOCUG00000011406	1 retrocopy	retro_ocun_575,
Otolemur garnettii	ENSOGAG00000011108	1 retrocopy	retro_ogar_2170,
Pteropus vampyrus	ENSPVAG00000010175	1 retrocopy	retro_pvam_633,
Ictidomys tridecemlineatus	ENSSTOG00000010607	1 retrocopy	retro_itri_241,
Tupaia belangeri	ENSTBEG00000008942	3 retrocopies	retro_tbel_1128, retro_tbel_216, retro_tbel_3310,
Tarsius syrichta	ENSTSYG00000001351	1 retrocopy	retro_tsyr_510,