RetrogeneDB ID: retro_cpor_944

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_36:2905439..2905827(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG12
• Ensembl ID: ENSCPOG00000007187
• Aliases: None
• Description: None

Sequence

>retro_cpor_944
TCTGCTCTACAGCTCATTCTGTCAGCTGAGACTGCTGGTGGCAAAGTACTTGGGGATCTGTCCCTGAAACAGCCACACAA
GAGTGCCCTTCTTCTGCTTCAGACAGAAGAACCTGTTTCAGGGACACCAAGAAAAATTTGACATACTGGTAAAGGCTGCG
GAGACACCCCTAAATGGAAACAAAGACGTGGGCTGTAGAGCAAAGGCTAACAATCCAAGGACTCACTGACTTCATCTGAC
AGTTCTTTAACTTGTGGCCTCTGAATAGTTGTTTATTTTTGTAAATCAATCTTTTGGACCTTCCCCAGACAAGAAGGTTG
GAATCCTCTATAGGTGTTTTAGCAATGGTGGTAAAAGAATCTTTGTTTACTGCAAATCTCAGATATGG

Alignment

ORF - retro_cpor_944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.62 %
• Parental protein coverage: 77.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVLQLPPSAVAAGGEGLGELSPETATPEP-PSAAVSPGTEEPAGDTKKKI-DVLLKAV-GDTPI-MKTKK
          S.LQL..SA..AG....G..........P..SA.....TEEP...T..KI.D.L.KA..GDTP..M.TK.
Retrocopy SALQLILSAETAG----GKVLGDLSLKQPHKSALLLLQTEEPVSGTPRKI>DILVKAA<GDTPK<METKT

Parental  WAVERTRTIQGLIDFIKKFLK-LVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCKSQAW
          WAVE...TIQGL.DFI..F...LVASE.LFI.VNQSF.PSPD..VG.LY.CF...GK....YCKSQ.W
Retrocopy WAVEQRLTIQGLTDFI*QFFN<LVASE*LFIFVNQSFGPSPDKKVGILYRCFSNGGKRIFVYCKSQIW

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	13.57 RPM
SRP017611_kidney	0.00 RPM	21.77 RPM
SRP017611_liver	0.00 RPM	19.28 RPM
SRP040447_lung	0.00 RPM	13.67 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_944 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_944 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944 ,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518, retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,