RetrogeneDB ID: retro_cpor_307

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_12:39133461..39133940(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000006631
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSCPOG00000008007
• Aliases: None
• Description: None

Sequence

>retro_cpor_307
CTGGCCGAGCAGGCTGAGCCATATGACGACATGGTTGAATCAATGAAGAAAGTAACAGGTATGGATGTGGAGCTGACGGC
TGAAGAAAGAAACCTCCTATCTGTTGCATATAAAAATGTGATTGGAGCTAGAAGAGCCTCCTGGAGAATAATCAGCAGCA
TTGAACAGAAAGAAGAAAACAAGGGAGAAGAAGATAAACTAAAAACGATTCGAGAATATCGGCAAATGGTTGAGACTGAG
CTAAAGTTATCTGTTGTGACATTCTGGATGTACTGGACAAACACCTCATTCCAGCAGCTAACACTGGCGAGTCCAGGGTT
TTCTATTATAAAATGAAAGGGGACTACCACAGGTATCTGGCTGAATTGGCCACAGGAAATGACAGGAAGGAGGCTGCAAA
GAACAGCCTAGTGGCTTATAAAGCTGCTAGTGATGTTGCAATGACAGAACCTCCACCAACGCATCGTATTCGTTTAGGT

Alignment

ORF - retro_cpor_307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.82 %
• Parental protein coverage: 62.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGYQAFSHLEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMI
          L..QA.....MVESMKKV.GMDVELT.EERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.EDKLK.I
Retrocopy LAEQAEPYDDMVESMKKVTGMDVELTAEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGEEDKLKTI

Parental  REYRQMVETELKL-ICCDILDVLDKHLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVA
          REYRQMVETELKL.ICCDILDVLDKHLIPAANTGES.VFYYKMKGDYHRYLAE.ATGNDRKEAA.NSLVA
Retrocopy REYRQMVETELKL<ICCDILDVLDKHLIPAANTGESRVFYYKMKGDYHRYLAELATGNDRKEAAKNSLVA

Parental  YKAASDIAMTELPPTHPIRLG
          YKAASD.AMTE.PPTH.IRLG
Retrocopy YKAASDVAMTEPPPTHRIRLG

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	0.12 RPM	254.74 RPM
SRP017611_kidney	0.00 RPM	148.45 RPM
SRP017611_liver	0.09 RPM	88.75 RPM
SRP040447_lung	0.13 RPM	117.15 RPM
SRP040447_skeletal_muscle	0.05 RPM	155.80 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_307 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_307 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 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Cavia porcellus	ENSCPOG00000008007	1 retrocopy	retro_cpor_307 ,
Cavia porcellus	ENSCPOG00000011321	4 retrocopies	retro_cpor_135, retro_cpor_1463, retro_cpor_616, retro_cpor_668,
Cavia porcellus	ENSCPOG00000020285	5 retrocopies	retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Felis catus	ENSFCAG00000011368	1 retrocopy	retro_fcat_1636,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,