RetrogeneDB ID: retro_cpor_25

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_54:2142693..2143266(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000023728
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000010655
• Aliases: None
• Description: None

Sequence

>retro_cpor_25
ATGGAAAAAGCAACAACAATCAAAGAAGCCTTAGCAATATGGGAAGAAGAAACTGGTCAGAGGCCATCTGAAGCCCAGGA
GATAAAGCTTTATGCCCAGATTCCCCCAATAGAGAAGATGGATGCCTCCTTATCCACACTTGCTAACTGCGAGAAGCTTT
CACTGTCTACAAATTGCATTGAAAGAATTGCCAACCTGAATGGCTTAAAAAACTTGAGGATCTTGTCTTTAGGAAGAAAC
AACATAAAGAACTTAAATGGACTGGAAGCTGTAGGAGACACGTTAGAAGAACTGTGGATCTCCTACAATTTTATTGAAAA
GTTGAAAGGGATCCATGTAATGAAACAATTGAAGATTCTCTACATGTCTAATAACCTGGTGAAAGAGTGGGCTGAGTTTG
TGAAGCTGTCAGAACTGCCGTGCCTGGAAGACCTGGTATTTGTCGGCAATCCTCTGGAAGAGAAACATTCTGCCGAAGGG
AACTGGATTGAGGAAGCAACCAAAAGAGTGCCCAAACTAAAAAAGCTGGAAGTTACTCCGGTAATTAAACAGGATGAGGA
AGAAAAAAATTAA

Alignment

ORF - retro_cpor_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.15 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KATTIKEALARWQKSDGXRPSEAKEIKLYAQIPPIEKMDASLSTLANCEKLSLSTNCIERIANLNGLKNL
          KATTIKEALA.W....G.RPSEA.EIKLYAQIPPIEKMDASLSTLANCEKLSLSTNCIERIANLNGLKNL
Retrocopy KATTIKEALAIWEEETGQRPSEAQEIKLYAQIPPIEKMDASLSTLANCEKLSLSTNCIERIANLNGLKNL

Parental  RILSLGRNNIKNLNGLEAVGDTLEELWISYNFIEKLKGIHVMKKLKILYMSNNLVKEWAEFVKLSELPCL
          RILSLGRNNIKNLNGLEAVGDTLEELWISYNFIEKLKGIHVMK.LKILYMSNNLVKEWAEFVKLSELPCL
Retrocopy RILSLGRNNIKNLNGLEAVGDTLEELWISYNFIEKLKGIHVMKQLKILYMSNNLVKEWAEFVKLSELPCL

Parental  EDLVFVGNPLEEKHSAEGNWIEEATKRVPKLKKLDGTPVIKQDEEEEN
          EDLVFVGNPLEEKHSAEGNWIEEATKRVPKLKKL..TPVIKQDEEE.N
Retrocopy EDLVFVGNPLEEKHSAEGNWIEEATKRVPKLKKLEVTPVIKQDEEEKN

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	0.81 RPM	6.15 RPM
SRP017611_kidney	0.10 RPM	3.14 RPM
SRP017611_liver	0.22 RPM	1.74 RPM
SRP040447_lung	0.83 RPM	2.40 RPM
SRP040447_skeletal_muscle	0.16 RPM	0.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_25 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_25 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015930	1 retrocopy	retro_btau_1190,
Cavia porcellus	ENSCPOG00000010655	1 retrocopy	retro_cpor_25 ,
Drosophila melanogaster	FBgn0033408	1 retrocopy	retro_dmel_26,