RetrogeneDB ID: retro_cpor_835

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_3:64586991..64587439(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2L3
• Ensembl ID: ENSCPOG00000006044
• Aliases: None
• Description: None

Sequence

>retro_cpor_835
ATGGCGGCCAGCAAGAGGCAGATGAAGGAGCTTGAAATGATCTTAAATTGTGGAAATAAAAACTTCTACAACATCGAGGC
TGATAAAGTTAATTTGCCACCTTGGCAAGAGCTTACTGTTCCTCATAGCCCTACATATAATAAAGGGCCCTTAGAATTGA
AATCAAGTTTCCAGCAGAGTATCCATTCAAACCACCGAAGATCACATGTAAAACAAAGATCTATCACCCAACATTGATGA
AAAAGGGTAAATTTGCCTGCTAGCAATTAGTGCTGAGGACCGGAAACCAACAACTAAGACTGACTAAGTAATCTAGTCCC
TCATAGCGCTGGTGAACCAACCCCAGCCCTAGCAACCATTCTGGGCACACCTAGCTGATGACTACTCTAAGGACCATAAA
ACACTCTGTAAGAATGCTGAAGAGTTAACAAAGAAATATAAGGAAAAA

Alignment

ORF - retro_cpor_835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.74 %
• Parental protein coverage: 97.4 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKG-AFRIEINFPAEYPFKPPKIT
          MAAS.R.MKELE.I..CG.KNF.NI..D..NL..WQ.L.VP..P.Y.KG.A.RIEI.FPAEYPFKPPKIT
Retrocopy MAASKRQMKELEMILNCGNKNFYNIEADKVNLPPWQELTVPHSPTYNKG<ALRIEIKFPAEYPFKPPKIT

Parental  FKTKIYH-PNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFCK
          .KTKIYH.PNIDEKG..CL..ISAE..KP.TKTD.VI.SLIALVN.PQP..P..A.LA..YSKD.K..CK
Retrocopy CKTKIYH<PNIDEKG*ICLLAISAEDRKPTTKTD*VI*SLIALVNQPQP*QPFWAHLADDYSKDHKTLCK

Parental  NAEEFTKKYGEK
          NAEE.TKKY.EK
Retrocopy NAEELTKKYKEK

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	25.77 RPM
SRP017611_kidney	0.00 RPM	40.72 RPM
SRP017611_liver	0.00 RPM	29.95 RPM
SRP040447_lung	0.00 RPM	28.07 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.32 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_835 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_835 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 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015284	1 retrocopy	retro_cfam_1090,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Cavia porcellus	ENSCPOG00000006044	2 retrocopies	retro_cpor_692, retro_cpor_835 ,
Equus caballus	ENSECAG00000019274	1 retrocopy	retro_ecab_116,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Myotis lucifugus	ENSMLUG00000001547	1 retrocopy	retro_mluc_32,
Monodelphis domestica	ENSMODG00000017665	2 retrocopies	retro_mdom_2029, retro_mdom_956,
Mus musculus	ENSMUSG00000038965	10 retrocopies	retro_mmus_1619, retro_mmus_1620, retro_mmus_2147, retro_mmus_2212, retro_mmus_2272, retro_mmus_2315, retro_mmus_3205, retro_mmus_3714, retro_mmus_541, retro_mmus_995,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pan troglodytes	ENSPTRG00000014114	1 retrocopy	retro_ptro_123,
Rattus norvegicus	ENSRNOG00000001862	4 retrocopies	retro_rnor_1602, retro_rnor_2633, retro_rnor_2799, retro_rnor_526,
Tetraodon nigroviridis	ENSTNIG00000010600	1 retrocopy	retro_tnig_16,
Takifugu rubripes	ENSTRUG00000003392	1 retrocopy	retro_trub_39,