RetrogeneDB ID: retro_cpor_985

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:18644767..18645172(+)
• Located in intron of: ENSCPOG00000003524

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSCPOG00000026329
• Aliases: None
• Description: None

Sequence

>retro_cpor_985
GCCTTTGAGAAGAGTGGATGGTTGCTACAACACGGTACTACTCTGAAGCACTGGAGGAAAAACTGGTTTGATCTGTGGTC
GGATGGTCACCTGCCCTACGAGGACACTCAGACACAGCGGAGTACTGAGCAGGAAGCCCATATGCCAGCGGACTGCATCA
ACATCCACACAGGGCACAAGTGGCGGGATAGTCAGCCTCCAGATGGGAAGCCAAAAGACTGTCCGCTTGGGATTGTTTGC
CGAGATGGAAAGAGGACCCATGTTTGTGCAGAAAGCACAGATGATTGTTTGACTTGGAAATTTACACTGTAGGATTCCAG
AACAAATACAGCATGCGTGGGCTCTGCTGTCCTGTGGGAAGAGACCAACGTGGCTTCCTCGCTGCTTCCGTAAGGGGGCT
ATGCT

Alignment

ORF - retro_cpor_985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.15 %
• Parental protein coverage: 60.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDDQTRQSIEDKVHMPVDCINIRIGPECRDIQPPDGK
          AF.KSGWLL...T.LK.W.KNWFDLWSDGHL.Y.D.QT..S.E...HMP.DCINI..G...RD.QPPDGK
Retrocopy AFEKSGWLLQHGTTLKHWRKNWFDLWSDGHLPYEDTQTQRSTEQEAHMPADCINIHTGHKWRDSQPPDGK

Parental  PKDCLLQIVCRDGKTISLCAESADDCLAWKLTLQDSRTNTACVGSPVLPEETVAASPPPPYMAYA
          PKDC.L.IVCRDGK....CAES.DDCL.WK.TL.DSRTNTACVGS.VL.EET..AS...P...YA
Retrocopy PKDCPLGIVCRDGKRTHVCAESTDDCLTWKFTL*DSRTNTACVGSAVLWEETNVASSLLP*GGYA

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	53.55 RPM
SRP017611_kidney	0.00 RPM	32.87 RPM
SRP017611_liver	0.00 RPM	5.92 RPM
SRP040447_lung	0.00 RPM	20.71 RPM
SRP040447_skeletal_muscle	0.00 RPM	20.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_985 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_985 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985 ,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,