RetrogeneDB ID: retro_cpor_218

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:20234449..20235020(-)
• Located in intron of: ENSCPOG00000002614

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX2
• Ensembl ID: ENSCPOG00000011099
• Aliases: None
• Description: None

Sequence

>retro_cpor_218
AATGCAGAATGTGTGTCTTCATCTGGTAAAGTATCTTTTATTCATGTGGGAAATCAAACAGTTTCACAACTTGGTCCTAT
ATTCAGTTCTTTAAAATCAAGGGCCATTGTTGTAGTGGTGGGTTGGACCAGACCACAAAGCAGAAATGAAGGCTTATGTG
GAATTAGTCAATATGCTGCTGACTGCAAAGTTTATCTTCAGTGGTATGATGAAGTTACAGGGCAGGCAGATTGCTCATGC
TAGGCATGGATCTCCTGACTCTTGGCCTCTGAATCATATTTTGGCCTATCAGAAACAGTAGGAAGTCAGCAAAAGATGAA
AGCTCTGGGATGGGGAAACAAGACTTTAGACCAGGTTCTAGATGTTGACCAGGGATGTCAAGCTCTTTCTCAAAGACTGG
AAACAACCATATTTCTTCAAAAGTGGCCTAATGATTTTGGTGCATTGGTATTTGGCCATCTGTACACCATTCTACCACGC
AATTGACCAAAGATAATCTTCTGAGAAGGTGAAAAGCTACAGCAAGCTCTTAACTTTCTGCAGAAGAGTTAAACATCCCT
ATTTTGAAAAC

Alignment

ORF - retro_cpor_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.31 %
• Parental protein coverage: 71.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NAEYMSPSGKVPFIH-GNQVVSELGPI-VQFVKAKGHCLSDGLDEV-QKAEMKAYMELVNNMLLTAE-LY
          NAE..S.SGKV.FIH.GNQ.VS.LGPI..QF.K.KGHC.S.GLD....KAEMKAY.ELVN.MLLTA...Y
Retrocopy NAECVSSSGKVSFIHVGNQTVSQLGPI<IQFFKIKGHCCSGGLDQT<HKAEMKAYVELVN-MLLTAK<VY

Parental  LQWCDEATVG-EITHARYGSPYPWPLNHILAYQKQWEV-KRKMKAIGWGNKTLDQVLEDVDQCCQALSQR
          LQW.DE.T....I.HAR.GSP..WPLNHILAYQKQ.EV...KMKA.GWGNKTLDQVL.DVDQ.CQALSQR
Retrocopy LQWYDEVTGQ>QIAHARHGSPDSWPLNHILAYQKQ*EV<QQKMKALGWGNKTLDQVL-DVDQGCQALSQR

Parental  LGTQPYFFNKQPTELDALVFGHLYTIL-TTQLTNDEL-SEKVKNYSNLLAFCRRIEQHYFED
          L.T...F..K.P....ALVFGHLYTIL.TTQLT.D.L.SEKVK.YS.LL.FCRR....YFE.
Retrocopy LET-TIFLQKWPNDFGALVFGHLYTIL<TTQLTKDNL<SEKVKSYSKLLTFCRRVKHPYFEN

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	15.36 RPM
SRP017611_kidney	0.00 RPM	29.84 RPM
SRP017611_liver	0.00 RPM	14.80 RPM
SRP040447_lung	0.00 RPM	14.68 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_218 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_218 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429,
Cavia porcellus	ENSCPOG00000011099	1 retrocopy	retro_cpor_218 ,
Dipodomys ordii	ENSDORG00000003848	2 retrocopies	retro_dord_159, retro_dord_192,
Homo sapiens	ENSG00000128654	1 retrocopy	retro_hsap_3780,
Macaca mulatta	ENSMMUG00000010185	1 retrocopy	retro_mmul_1643,
Nomascus leucogenys	ENSNLEG00000006020	1 retrocopy	retro_nleu_1117,
Pan troglodytes	ENSPTRG00000012674	1 retrocopy	retro_ptro_2561,
Sarcophilus harrisii	ENSSHAG00000016381	1 retrocopy	retro_shar_162,