RetrogeneDB ID: retro_cpor_375

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_137:2685961..2686446(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025231
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTAP
• Ensembl ID: ENSCPOG00000000825
• Aliases: None
• Description: methylthioadenosine phosphorylase [Source:HGNC Symbol;Acc:7413]

Sequence

>retro_cpor_375
CAGACCTTCTATGATGGAAGTCATTCCTGTGCCAGAGGAGTGTGCCACATTCCAGTGGCCGAACCATTTTGCCCCAAAAC
AAGAGAGGTCCTGATAGAGACCTCTAAGAAGCTAGGACTGCGGTGCCACCCAAAGGGAACAATGATCACAATCGAGGGAC
CCCGTTTTAGCTCCACGGCAGAAAGCCTCATGTTTTGCACATGGGGAGCAGATGTTATCAATAAGACCACAGTTCCAGAG
GTAGTTCTTGCTAAAGAGGCTGGGATTTGCTATGCAAGCATCGCCATGGCAACTGATTACGACTGCTGGAAGGAGCTAGA
GGAAACAGTTTCAGTTGATCGGGTTTTAAAGACCCTGAAGGAAAATGCTAATAAAGCCAAAAGCTTACTCCTCACCACAT
ACCTCAGATCGGGTTTATGGAATGTTCGGAAACCTTCCATAACCTGAAGAATATGGCTCAGTTTTCAGTTTTATTACCAA
GACAC

Alignment

ORF - retro_cpor_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.09 %
• Parental protein coverage: 59.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTFYDGSHSCARGVCHIPVAEPFCPKTREVLIETSKKLGLRCHPKGTMITIEGPRFSSRAESLMFRTWGA
          QTFYDGSHSCARGVCHIPVAEPFCPKTREVLIETSKKLGLRCHPKGTMITIEGPRFSS.AESLMF.TWGA
Retrocopy QTFYDGSHSCARGVCHIPVAEPFCPKTREVLIETSKKLGLRCHPKGTMITIEGPRFSSTAESLMFCTWGA

Parental  DVINMTTVPEVVLAKEAGICYASIAMATDYDCWKEHEETVSVDRVLKTLKENANKAKSLLLTT-IPQIGS
          DVIN.TTVPEVVLAKEAGICYASIAMATDYDCWKE.EETVSVDRVLKTLKENANKAKSLLLTT.IPQIG.
Retrocopy DVINKTTVPEVVLAKEAGICYASIAMATDYDCWKELEETVSVDRVLKTLKENANKAKSLLLTT<IPQIGF

Parental  MEWSETLHNLKNMAQFSVLLPRH
          ME.SET.HNLKNMAQFSVLLPRH
Retrocopy MECSETFHNLKNMAQFSVLLPRH

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	1.84 RPM
SRP017611_kidney	0.31 RPM	12.25 RPM
SRP017611_liver	0.17 RPM	8.88 RPM
SRP040447_lung	0.03 RPM	18.16 RPM
SRP040447_skeletal_muscle	0.01 RPM	4.62 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_375 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_375 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375 ,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,