RetrogeneDB ID: retro_cpor_322

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_124:3310224..3310806(+)
• Located in intron of: ENSCPOG00000004647

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR45L
• Ensembl ID: ENSCPOG00000005657
• Aliases: None
• Description: None

Sequence

>retro_cpor_322
AAGAAAAAGAAACAAGAATTTTGGGAAAGAGGAGTTGGCTGTATAGAAATATTATTTCATTGTAAATATTCAGATTTCAT
TGGAGGTGGGAAAAAGCTCAAATGTCCTCCTAATAAAGTGATGATTTGGAAGAGCTGAAGAAGACTATTACAAAGGCAGG
GTTCTCTATGGAGGTCTAGGCAGTCAAGTTACAACATGATAGAAATAGTGATTGTTTTGGACTCATGATTAAGGTGTTCA
CATTCACACACATTTTCCACCAGCTGCTCATCTTTGAAACTTGTCATAAACCTAAAGGCCTTTGTGTCTATGACCCAGAA
GTACACATTCCTCCTTGTCTTCCTGGGGACTCACACAGGCCATGTGTAGGTAGGTCCTGACCAGTATCTAGAAGCCACTT
GTGGACATTGCTCAGGATGGTTTCCTGAGCTGCATCACTTCAATCTGCAAGGAACAAGAATTACAACTACCTCTGAAAAG
GAAACCCTTATAAGAATTTGGTACTTCCTCAAGGCATAATTGCTACAAAGAGGCTCTCAAACAGCTAATATCTACTGTAT
CAACTTCAATCAGCATGCTTCC

Alignment

ORF - retro_cpor_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EKEKQEFLEGGVGHVEMLFRCNYLALVGGGKKPKYPPNKVMIW-DDLKKKTVIEIEFSTEVKAVKLRRDR
          .K.KQEF.E.GVG..E.LF.C.Y....GGGKK.K.PPNKVMIW...LKK.T.....FS.EV.AVKL..DR
Retrocopy KKKKQEFWERGVGCIEILFHCKYSDFIGGGKKLKCPPNKVMIW<EELKK-TITKAGFSMEV*AVKLQHDR

Parental  -IVVVLDS-MIKVFTFTHNPHQLHVFETCYNPKGLCV-LCPNSNNSLLAFPGTHTGHVQLVDLASTEKPP
          .IV.VLDS.MIKVFTFTH..HQL..FETC..PKGLCV.L.P.S..S.L...G........V.L.S..KP.
Retrocopy >IVIVLDS<MIKVFTFTHIFHQLLIFETCHKPKGLCV<L*PRSTHSSLSSWGLTQAMCR*V-LTSI*KPL

Parental  VDIPAHEGVLSCIA-LNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDAS
          VDI.A..G.LSCI...NLQGTRI.T.SEK.TLIRI.......L.Q...RGSQ.ANIYCINFNQ.AS
Retrocopy VDI-AQDGFLSCIT<FNLQGTRITTTSEKETLIRIWYFLKA*LLQ---RGSQTANIYCINFNQHAS

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	26.29 RPM
SRP017611_kidney	0.00 RPM	18.74 RPM
SRP017611_liver	0.00 RPM	11.71 RPM
SRP040447_lung	0.00 RPM	29.91 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.48 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_322 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_322 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322 ,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,