RetrogeneDB ID: retro_cpor_574

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:19034112..19034553(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXI1
• Ensembl ID: ENSCPOG00000022901
• Aliases: None
• Description: None

Sequence

>retro_cpor_574
ACACACAGTGAGCTGGAAAAAAATCAGCGAACTCAACTGCACCTACATCTAGAACGCTTGAAAGTTCTGATTCCTCTAGT
AGGATCAAACTGTACCAAGCACACAATGCTTAGTTTGCTCAAAAAAGCCAAAGCACGTATCAGGAAACTTGAAGAAGCTG
AAAGGAAGAGCCAGCACCAGCTGGAGAACTTGGAACGAGAACAGAGAATTTTAAAGCGATGACTAGAACAGCTGCAGGGT
CCTCAAGAGATGGAATGAATACGAATGGACAGCATTGGATCAACTAATTCTTCAGATCATTCTGACTCAGAGTGAGAGGA
GATCGAATGAAAGCACAGAGTTCTCCCACAGAGAAGTGGACAATATAAGTATCACCCGCATAGTGACATTGATGACCCCA
GCAGTATTGGGAGTGATGAGGGTTACTCCAGTGCCAGTGTC

Alignment

ORF - retro_cpor_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.55 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  THNELEKNRRAHLRLCLERLKVLIPL-GPDCTRHTTLGLLNKAKAHIKKLEEAERKSQHQLENLEREQRF
          TH.ELEKN.R..L.L.LERLKVLIPL.G..CT.HT.L.LL.KAKA.I.KLEEAERKSQHQLENLEREQR.
Retrocopy THSELEKNQRTQLHLHLERLKVLIPLVGSNCTKHTMLSLLKKAKARIRKLEEAERKSQHQLENLEREQRI

Parental  LKRRLEQLQGPQEMERIRMDSIGSTISSDRSDSEREEIEV-DVESTEFSHGEVDNISTTSI-SDIDDHSS
          LKR.LEQLQGPQEME.IRMDSIG...S...SD....E.E....ESTEFSH.EVDNIS.T.I.SDIDD.SS
Retrocopy LKR*LEQLQGPQEME*IRMDSIG---STNSSDHSDSE*EE>SNESTEFSHREVDNISITRI<SDIDDPSS

Parental  LQSIGSDEGYSSASV
          ...IGSDEGYSSASV
Retrocopy ---IGSDEGYSSASV

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	14.09 RPM
SRP017611_kidney	0.00 RPM	7.85 RPM
SRP017611_liver	0.00 RPM	2.87 RPM
SRP040447_lung	0.00 RPM	10.09 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.32 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_574 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_574 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574 ,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948,
Sus scrofa	ENSSSCG00000022128	1 retrocopy	retro_sscr_947,
Vicugna pacos	ENSVPAG00000003400	2 retrocopies	retro_vpac_483, retro_vpac_595,