RetrogeneDB ID: retro_cpor_30

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:13816843..13817731(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000022272
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000007690
• Aliases: None
• Description: None

Sequence

>retro_cpor_30
ATGGCCAGTGTGCTCTCTAACAGGGCCAGACTGGTTTCTTACCTCCCTGGATTTTACTCGTTAGTTAAAAGAGTTGTCAA
CCCAAGAGCCTTTTCAACAGCAGGATCTTCAGGTTCTGATGAATCTCATGTGGCCACCTCATCCCCAGATATATGCTCTC
GAACAGTGTGGCCTGATGAAACTATGGGACCTTTTGGACCTCAAGATCAGCGTTTCCAGCTTCCTGGGAATGTAAGCTTT
GAGTGTCATCTCAATGGGACTGCTGTACAAAAGAAAAGCCAAGGTCATAAAATTTTACCTGATGTTCTGGCAGAACCTTT
ATCAACTGAAAGACATGAGTTTGTGATGGCGCAATATGTTAATGAATTTCAGGGTAATAATGAGCCTGTAGAACAAGAAA
TTAACAGTGCAGAAACTTATTTCGAAAGTGCCAGAGTAGAGTGTGTAATCCAGACATGTCCAGAATTGCTTCGGAGAGAC
TTTGAATCACTATTTCCAGAAGTAGCTAATGGCAAACTAATGATTCTGACTGTAACTCAGAAAACTAAGAATGATATGAC
TGTTTGGAGTGAGGAGGTAGAACTTGAAAGAGAAACACTCTTAGAAAAGTTCATTAATGGTGCTAAGGAAATTTGCTATG
CTCTTCGAGCAGAAGGCTACTGGGCTGACTTCATTGACCCATCATCTGGTGTGGCATTTTTTGGACCATATTCAAACAAC
ACTCTTTTTGAAACAGATGAACGCTACCGACATTTAGGGTTCTCTGTTGATGATCTTGGCTGCTGCAAAGTAATCCGCCA
TAATCTCTGGGGTACCCATGTGTTTGTAGGAAGTATCTTCACTAATGCAACACCAGACAGCCATATTATGAAGAAATTAA
GTGGAAAT

Alignment

ORF - retro_cpor_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLSNRARLVSYLPGFYSLVKRVVNPRAFSTAGSSGSDESHVATSSPDICSRTVWPDETMGPFGPQDQRFQ
          VLSNRARLVSYLPGFYSLVKRVVNPRAFSTAGSSGSDESHVATSSPDICSRTVWPDETMGPFGPQDQRFQ
Retrocopy VLSNRARLVSYLPGFYSLVKRVVNPRAFSTAGSSGSDESHVATSSPDICSRTVWPDETMGPFGPQDQRFQ

Parental  LPGNVGFECHLNGTAVQKKSQGHKILPDVLAEPLSTERHEFVMAQYVNEFQGNNEPVEQEINSAETYFES
          LPGNV.FECHLNGTAVQKKSQGHKILPDVLAEPLSTERHEFVMAQYVNEFQGNNEPVEQEINSAETYFES
Retrocopy LPGNVSFECHLNGTAVQKKSQGHKILPDVLAEPLSTERHEFVMAQYVNEFQGNNEPVEQEINSAETYFES

Parental  ARVECVIQTCPELLRRDFESLFPEVANGKLMILTVTQKTKNDMTVWSEEVELERETLLEKFINGAKEICY
          ARVECVIQTCPELLRRDFESLFPEVANGKLMILTVTQKTKNDMTVWSEEVELERETLLEKFINGAKEICY
Retrocopy ARVECVIQTCPELLRRDFESLFPEVANGKLMILTVTQKTKNDMTVWSEEVELERETLLEKFINGAKEICY

Parental  ALRAEGYWADFIDPSSGVAFFGPYSNNTLFETDERYRHLGFSVDDLGCCKVIRHNLWGTHVFVGSIFTNA
          ALRAEGYWADFIDPSSGVAFFGPYSNNTLFETDERYRHLGFSVDDLGCCKVIRHNLWGTHVFVGSIFTNA
Retrocopy ALRAEGYWADFIDPSSGVAFFGPYSNNTLFETDERYRHLGFSVDDLGCCKVIRHNLWGTHVFVGSIFTNA

Parental  TPDSHIMKKLSGN
          TPDSHIMKKLSGN
Retrocopy TPDSHIMKKLSGN

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	1.09 RPM	11.04 RPM
SRP017611_kidney	3.35 RPM	39.89 RPM
SRP017611_liver	3.18 RPM	27.81 RPM
SRP040447_lung	2.02 RPM	21.99 RPM
SRP040447_skeletal_muscle	3.82 RPM	38.49 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_30 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_30 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003086	2 retrocopies	retro_cjac_4082, retro_cjac_4101,
Cavia porcellus	ENSCPOG00000007690	1 retrocopy	retro_cpor_30 ,
Homo sapiens	ENSG00000168288	2 retrocopies	retro_hsap_4716, retro_hsap_865,
Gorilla gorilla	ENSGGOG00000027348	1 retrocopy	retro_ggor_704,
Macaca mulatta	ENSMMUG00000005633	1 retrocopy	retro_mmul_1058,
Monodelphis domestica	ENSMODG00000003566	2 retrocopies	retro_mdom_1749, retro_mdom_620,
Mustela putorius furo	ENSMPUG00000000323	1 retrocopy	retro_mputfur_1253,
Nomascus leucogenys	ENSNLEG00000010795	2 retrocopies	retro_nleu_1988, retro_nleu_426,
Otolemur garnettii	ENSOGAG00000034385	4 retrocopies	retro_ogar_3266, retro_ogar_356, retro_ogar_688, retro_ogar_813,
Pan troglodytes	ENSPTRG00000012525	1 retrocopy	retro_ptro_599,
Ictidomys tridecemlineatus	ENSSTOG00000021576	1 retrocopy	retro_itri_1809,
Tarsius syrichta	ENSTSYG00000009075	1 retrocopy	retro_tsyr_1690,