RetrogeneDB ID: retro_cpor_483

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_167:147195..147960(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K1
• Ensembl ID: ENSCPOG00000003053
• Aliases: None
• Description: None

Sequence

>retro_cpor_483
AACCAGATCACCGTCTAGCTGAAGGTGCTGCATGCATGCAACTCGCTGCCCGTTATGAACCTCCACGGGGGTCCCTGCAG
TGACGGGGAGGTCAGTACCAGCATGGAGCACACTGATAGGGGTTCTCTGGATTAAGTCTTGAGGATCTCTGGATGAATTC
CTGAATACATTTTAGGAGACGTTAGCATTGCTATAATACAGGGCCTGACATGTCCGAGGGAAAGGCACAAGATACGCGGA
GAAGTCAAGTCCTCCAGCACCCTGGTCAGCTCCTGGGGAGCGCTCAGGCTGTGTGACCTCAGGGTCAGCGTGCAGCTCAT
CCACTCCATGGCCTACTCCTTTGTGGGCGCCAGGTCCTACATGTTGCCAGAACGACTCCACAGCTCCTATCACTGGGTGC
AGCCAGGCATCTGGAGCACGGGGCTGTCTCTAGTGGAGATGGCAGTCAGTAAGCACCCCACTCTCATCTGGACACCAAGG
AGCTGGAGCTGATGTGTGAGTGGCAGATGGAGGGAACTGCGGCAGAGACCCCTCCCAGGTCCAGGAACCTGGGGAGACCT
CTCAGTTCCTATGGGGTGGACAACTGGCCTCTCACGTCAGTTTTTGAGCTGCTGGGTTACAAAGTTAATGAGTCACCTCC
AAAACTGCCCAGCGGAGTGACCAATCTGGAATTTCAGGATTTTGTAAATAAGTGCTTCATTGTAGAATCCTGTAGAGAGA
GCAGACTGGACACAGCTCGTAGCTCATGCTTTCACCAAGGGGTCC

Alignment

ORF - retro_cpor_483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.85 %
• Parental protein coverage: 65.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLT
          NQI...L.VLH.CNS.......G...SDGE.S..MEH.D.GSLD.VL...G.IPE.ILG.VSIA.I.GLT
Retrocopy NQITV*LKVLHACNSLPVMNLHGGPCSDGEVSTSMEHTDRGSLD*VLRISG*IPEYILGDVSIAIIQGLT

Parental  YLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWS
          ..RE.HKI....VK.S..LV.S.G...LCD..VS.QLI.SMA.SFVG.RSYM.PERL......VQ..IWS
Retrocopy CPRERHKI-RGEVKSSSTLVSSWGALRLCDLRVSVQLIHSMAYSFVGARSYMLPERLHSSYHWVQPGIWS

Parental  MGLSLVEMAVGRY-PIPPPDAKELELVFGCQVEGDAAEMPPRPRTPGRPLSSYGMDSRPPMAIFELLDYI
          .GLSLVEMAV....P....D.KELEL....Q.EG.AAE.PPR.R..GRPLSSYG.D..P....FELL.Y.
Retrocopy TGLSLVEMAVSKH<PHSHLDTKELELMCEWQMEGTAAETPPRSRNLGRPLSSYGVDNWPLTSVFELLGYK

Parental  VNEPPPKLPSGVFSLEFQDFVNKCLIK-NPAERADLKQLMVHAFIKRS
          VNE.PPKLPSGV..LEFQDFVNKC.I..NP.ERAD..QL..HAF.K.S
Retrocopy VNESPPKLPSGVTNLEFQDFVNKCFIV>NPVERADWTQLVAHAFTKGS

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	119.40 RPM
SRP017611_kidney	0.00 RPM	152.22 RPM
SRP017611_liver	0.00 RPM	18.02 RPM
SRP040447_lung	0.00 RPM	65.55 RPM
SRP040447_skeletal_muscle	0.00 RPM	45.98 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_483 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_483 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
Bos taurus	ENSBTAG00000033983	1 retrocopy	retro_btau_1416,
Cavia porcellus	ENSCPOG00000003053	1 retrocopy	retro_cpor_483 ,
Gorilla gorilla	ENSGGOG00000003687	1 retrocopy	retro_ggor_2650,
Macaca mulatta	ENSMMUG00000016840	1 retrocopy	retro_mmul_2285,
Otolemur garnettii	ENSOGAG00000015876	1 retrocopy	retro_ogar_1598,
Ochotona princeps	ENSOPRG00000007770	1 retrocopy	retro_opri_846,
Pongo abelii	ENSPPYG00000006576	2 retrocopies	retro_pabe_3092, retro_pabe_3249,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676,