RetrogeneDB ID: retro_cpor_1145

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:60932860..60933492(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX6
• Ensembl ID: ENSCPOG00000006862
• Aliases: None
• Description: None

Sequence

>retro_cpor_1145
AATGAGTTTTCTGTTGTTTGACAACATGCAGAATTTATCTGGCTTCAAGATTCTTTTGTTGAAAATGAAGACTATGTATG
TTATATCACTCCTCCAGCACCACCGAGGCCTGATTTTGCTGTTTCATGCAAAAAGCTACAGAAGCTTGGAGAAGGGGAAG
GGTCAATGACAAAGGAAGAATTCACAAAAATGAAACAGGAACTAGAAGCTGAGTATTTGGCAACATTCAAGAATACAGTG
GCAAGACATGAACTGTTCCTGTGTCATGTGGTAGCTCATCCTATTTTGAAGAAAGATTTAAATTTCTATGTCTTCTTGGA
ATATAATCAAGATTTAAGTGTTTCAGGAAAAAATAAAACAGAAAAACTTGAAGATTTCTCTTAAAATATGATCAGGTCAG
CAGACGTAGTCATTGTTTCAGGCTAACGGACATAGATGATTTCTACGAGCATAAACAAAAATTTCTTTTAGAATATCATA
ATGGAATTAAGGATACATCTGCTAAATTTGATAGGATGACAAGATCCCACAAAAGTGTTGCAGAGGATTACAACAGAATT
AGTTCTTCATTATATGTTTTAGGAACTCAGGATTCTATTAACATATGCAAGTTTTTTCTCAACGTTTTAGAA

Alignment

ORF - retro_cpor_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 50.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NEFSVVRQHEEFIWLHDSFVENEDYAGYIIPPAPPRPDFDASREKLQKLGEGEGSMTKEEFTKMKQELEA
          NEFSVV.QH.EFIWL.DSFVENEDY..YI.PPAPPRPDF..S..KLQKLGEGEGSMTKEEFTKMKQELEA
Retrocopy NEFSVV*QHAEFIWLQDSFVENEDYVCYITPPAPPRPDFAVSCKKLQKLGEGEGSMTKEEFTKMKQELEA

Parental  EYLAIFKKTVAMHEVFLCRVAAHPILRKDLNFHVFLEYNQDLSVRGKNKKEKLEDFFKNMVKSADGVIVS
          EYLA.FK.TVA.HE.FLC.V.AHPIL.KDLNF.VFLEYNQDLSV.GKNK.EKLEDF..NM..SAD.VIVS
Retrocopy EYLATFKNTVARHELFLCHVVAHPILKKDLNFYVFLEYNQDLSVSGKNKTEKLEDFS*NMIRSADVVIVS

Parental  G-VKDVDDFFEHERTFLLEYHNRVKDASAKSDRMTRSHKSAADDYNRIGSSLYALGTQDSTDICKFFLKV
          G...D.DDF.EH...FLLEYHN..KD.SAK.DRMTRSHKS.A.DYNRI.SSLY.LGTQDS..ICKFFL.V
Retrocopy G<LTDIDDFYEHKQKFLLEYHNGIKDTSAKFDRMTRSHKSVAEDYNRISSSLYVLGTQDSINICKFFLNV

Parental  SE
          .E
Retrocopy LE

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	19.73 RPM
SRP017611_kidney	0.00 RPM	64.17 RPM
SRP017611_liver	0.00 RPM	21.81 RPM
SRP040447_lung	0.00 RPM	36.85 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.62 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1145 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1145 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012873	1 retrocopy	retro_btau_870,
Cavia porcellus	ENSCPOG00000006862	1 retrocopy	retro_cpor_1145 ,
Nomascus leucogenys	ENSNLEG00000003310	1 retrocopy	retro_nleu_3063,
Pongo abelii	ENSPPYG00000005736	2 retrocopies	retro_pabe_1668, retro_pabe_1698,
Pan troglodytes	ENSPTRG00000006253	1 retrocopy	retro_ptro_1362,