RetrogeneDB ID: retro_cpor_1302

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_67:1237081..1237436(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UXT
• Ensembl ID: ENSCPOG00000009154
• Aliases: None
• Description: None

Sequence

>retro_cpor_1302
CCAAAGGAGCTCATCATGGTGAAGCTCCCTAAATGGCGGGTGGTGGAAGCCACCAGGGAGAAAGTACTGAGCCATGAGGC
CTTCATCAGTGACTTGTTGCAGCGGGATTTGGGAAAAAGTGCTGGACCATTGAGACAAGGTATATGAGCAGCTGGGCAAA
TACCTTCAACCAAAAAATGTCATTGAGCAGCTCCAGAAAACTAAGCACTCAGAGTTATATATGCAGGTGGTTTTGGACTG
TAACTTCGTTGACACAATGGTCTCTGATACTTCACACATCAAGATGGCGCTGGGATATGGTTTCTTCTTAGAATTGATGT
TGGCAGAAGCTTTCATGTTCATTGATCACAGAGCT

Alignment

ORF - retro_cpor_1302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 70.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQELIMATPPKRRAVETTGEKVLRYEAFISDVLQRDL-QKVLDHRDKIYEQLAKYLQLKNVIERLQETKH
          P.ELIM...PK.R.VE.T.EKVL..EAFISD.LQRDL..KVLDH.DK.YEQL.KYLQ.KNVIE.LQ.TKH
Retrocopy PKELIMVKLPKWRVVEATREKVLSHEAFISDLLQRDL>EKVLDH*DKVYEQLGKYLQPKNVIEQLQKTKH

Parental  SELYMQVDLGCNFFVDTVVSDTSRIYVALGYGFFLELTLAEALKFIDRKS
          SELYMQV.L.CN.FVDT.VSDTS.I..ALGYGFFLEL.LAEA..FID...
Retrocopy SELYMQVVLDCN-FVDTMVSDTSHIKMALGYGFFLELMLAEAFMFIDHRA

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	2.59 RPM
SRP017611_kidney	0.00 RPM	10.47 RPM
SRP017611_liver	0.00 RPM	8.57 RPM
SRP040447_lung	0.00 RPM	6.58 RPM
SRP040447_skeletal_muscle	0.01 RPM	4.47 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1302 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1302 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009154	1 retrocopy	retro_cpor_1302 ,
Dipodomys ordii	ENSDORG00000001025	1 retrocopy	retro_dord_627,
Erinaceus europaeus	ENSEEUG00000006151	1 retrocopy	retro_eeur_543,
Macropus eugenii	ENSMEUG00000003352	1 retrocopy	retro_meug_59,
Microcebus murinus	ENSMICG00000016263	1 retrocopy	retro_mmur_1156,
Mustela putorius furo	ENSMPUG00000013405	1 retrocopy	retro_mputfur_999,
Mus musculus	ENSMUSG00000001134	3 retrocopies	retro_mmus_1424, retro_mmus_1766, retro_mmus_715,
Rattus norvegicus	ENSRNOG00000009893	5 retrocopies	retro_rnor_521, retro_rnor_522, retro_rnor_683, retro_rnor_692, retro_rnor_882,
Tarsius syrichta	ENSTSYG00000012719	2 retrocopies	retro_tsyr_237, retro_tsyr_778,