RetrogeneDB ID: retro_cpor_1007

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:13186840..13187228(+)
• Located in intron of: ENSCPOG00000002442

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSCPOG00000014102
• Aliases: None
• Description: None

Sequence

>retro_cpor_1007
ATTCCTGCCTTCCCTGAGTCAGACAACCTTTTCAAAAGGATAGGGACCATCCATGGAGCACCTGATACAGAGTATGAAGA
CCTGCAGTACAAGCTCTCTCTCCCTGGAGTCCCCCAGTGGCTACCCTTACAACACATCCACAGTGAAGTTGCTTACTCCC
TGCTACCAACCCAATGTGGACACCCAGGGCAACATCTGCCTGGATGTCCAGGACAAATGGTCCGCCTTGTACAACATGAG
GACTATCCTGTCTATCCAGAGCCTGGTAGGAGAAACCAACATTGATAGTCCTTTGAACACACATGCTGCAGAGTTTTGAA
AAAACCGCACAGCTTTTAAGAAGTACCTGCAAGAAACCCACTCAAAGCAAGTCTCTAGCCAAGAGCCC

Alignment

ORF - retro_cpor_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 72.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISAFPESDNLFKWIGTIHGAAGTVYEDLRYKLSLE-FPSGYP-YNAPTVKFLTPCYHPNVDTQGNICLDI
          I.AFPESDNLFK.IGTIHGA..T.YEDL.YKLSL...P...P.YN..TVK.LTPCY.PNVDTQGNICLD.
Retrocopy IPAFPESDNLFKRIGTIHGAPDTEYEDLQYKLSLPGVPQWLP>YNTSTVKLLTPCYQPNVDTQGNICLDV

Parental  LKDKWSALYDVRTILLSIQSLLGEPNIDSPLNTHAAELWKNPTAFKKYLQETYSKQVSSQEP
          ..DKWSALY..RTI.LSIQSL.GE.NIDSPLNTHAAE..KN.TAFKKYLQET.SKQVSSQEP
Retrocopy -QDKWSALYNMRTI-LSIQSLVGETNIDSPLNTHAAEF*KNRTAFKKYLQETHSKQVSSQEP

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	0.63 RPM
SRP017611_kidney	0.00 RPM	2.09 RPM
SRP017611_liver	0.00 RPM	1.00 RPM
SRP040447_lung	0.00 RPM	6.89 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1007 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1007 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 19 parental genes, and 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005054	1 retrocopy	retro_chof_902,
Cavia porcellus	ENSCPOG00000014102	2 retrocopies	retro_cpor_1007 , retro_cpor_211,
Dipodomys ordii	ENSDORG00000011774	4 retrocopies	retro_dord_157, retro_dord_386, retro_dord_421, retro_dord_84,
Echinops telfairi	ENSETEG00000012346	18 retrocopies	retro_etel_1212, retro_etel_1500, retro_etel_1560, retro_etel_157, retro_etel_1634, retro_etel_1729, retro_etel_1853, retro_etel_1856, retro_etel_2013, retro_etel_221, retro_etel_321, retro_etel_324, retro_etel_400, retro_etel_628, retro_etel_689, retro_etel_764, retro_etel_824, retro_etel_909,
Homo sapiens	ENSG00000175063	3 retrocopies	retro_hsap_1474, retro_hsap_1922, retro_hsap_2935,
Gorilla gorilla	ENSGGOG00000026061	3 retrocopies	retro_ggor_1130, retro_ggor_1402, retro_ggor_2035,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Myotis lucifugus	ENSMLUG00000006715	4 retrocopies	retro_mluc_2164, retro_mluc_2220, retro_mluc_600, retro_mluc_636,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mus musculus	ENSMUSG00000001403	5 retrocopies	retro_mmus_1344, retro_mmus_1593, retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Ochotona princeps	ENSOPRG00000014284	4 retrocopies	retro_opri_1009, retro_opri_1055, retro_opri_222, retro_opri_50,
Pongo abelii	ENSPPYG00000011071	4 retrocopies	retro_pabe_1155, retro_pabe_1221, retro_pabe_1589, retro_pabe_2519,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,
Pteropus vampyrus	ENSPVAG00000000369	1 retrocopy	retro_pvam_423,
Rattus norvegicus	ENSRNOG00000015131	5 retrocopies	retro_rnor_1390, retro_rnor_2131, retro_rnor_2470, retro_rnor_719, retro_rnor_864,
Sarcophilus harrisii	ENSSHAG00000002117	1 retrocopy	retro_shar_832,
Tursiops truncatus	ENSTTRG00000015987	1 retrocopy	retro_ttru_1752,