RetrogeneDB ID: retro_cpor_1368

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_73:7204416..7204622(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUTF2
• Ensembl ID: ENSCPOG00000003521
• Aliases: None
• Description: None

Sequence

>retro_cpor_1368
ATTCATCCATCATGCCTTACATGAGGATGACAGCACTTACAGGACGAATCTGTCGTTGTAGAGAAGTTGTTGATCCTTCC
ATTCCTGAAAATCCAGCACAGCATCAAGCACTGAACCATCAGCCTATACCAGACAGCTGCATCAGCATGGCTGTGGGCCA
GTTCTGGGCCAATGAAGACCCCATCGTGGGGTTCCACCAGATGTTT

Alignment

ORF - retro_cpor_1368 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.38 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSIT-AQDHQPTPDSCIISMVVGQLKADEDPIMGFHQM
          I..SCLT...Q..Q.....VEKL..LPF.KIQHSI..A..HQP.PDSCI.SM.VGQ..A.EDPI.GFHQM
Retrocopy IHPSCLT*G*QHLQDESVVVEKLLILPFLKIQHSIK<ALNHQPIPDSCI-SMAVGQFWANEDPIVGFHQM

Parental  F
          F
Retrocopy F

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	0.12 RPM	13.98 RPM
SRP017611_kidney	0.10 RPM	23.14 RPM
SRP017611_liver	0.00 RPM	9.92 RPM
SRP040447_lung	0.13 RPM	25.67 RPM
SRP040447_skeletal_muscle	0.01 RPM	36.33 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1368 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1368 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 18 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017548	5 retrocopies	retro_amel_1225, retro_amel_134, retro_amel_1485, retro_amel_415, retro_amel_445,
Bos taurus	ENSBTAG00000006414	2 retrocopies	retro_btau_1573, retro_btau_881,
Cavia porcellus	ENSCPOG00000003521	1 retrocopy	retro_cpor_1368 ,
Erinaceus europaeus	ENSEEUG00000003470	2 retrocopies	retro_eeur_149, retro_eeur_571,
Gorilla gorilla	ENSGGOG00000023925	5 retrocopies	retro_ggor_1032, retro_ggor_2152, retro_ggor_279, retro_ggor_2806, retro_ggor_3028,
Macropus eugenii	ENSMEUG00000009874	11 retrocopies	retro_meug_1023, retro_meug_136, retro_meug_1539, retro_meug_1585, retro_meug_1778, retro_meug_2140, retro_meug_253, retro_meug_282, retro_meug_352, retro_meug_676, retro_meug_748,
Myotis lucifugus	ENSMLUG00000025175	3 retrocopies	retro_mluc_1265, retro_mluc_2194, retro_mluc_911,
Macaca mulatta	ENSMMUG00000012038	6 retrocopies	retro_mmul_1160, retro_mmul_1270, retro_mmul_2127, retro_mmul_2169, retro_mmul_2593, retro_mmul_27,
Monodelphis domestica	ENSMODG00000005517	6 retrocopies	retro_mdom_1031, retro_mdom_1291, retro_mdom_1488, retro_mdom_1489, retro_mdom_1903, retro_mdom_37,
Mus musculus	ENSMUSG00000008450	1 retrocopy	retro_mmus_232,
Oryctolagus cuniculus	ENSOCUG00000006322	1 retrocopy	retro_ocun_115,
Otolemur garnettii	ENSOGAG00000015568	2 retrocopies	retro_ogar_2713, retro_ogar_2811,
Rattus norvegicus	ENSRNOG00000018945	4 retrocopies	retro_rnor_1149, retro_rnor_1616, retro_rnor_2427, retro_rnor_545,
Sarcophilus harrisii	ENSSHAG00000006100	1 retrocopy	retro_shar_274,
Sus scrofa	ENSSSCG00000030295	3 retrocopies	retro_sscr_1223, retro_sscr_710, retro_sscr_740,
Tupaia belangeri	ENSTBEG00000011016	1 retrocopy	retro_tbel_7,
Tursiops truncatus	ENSTTRG00000009251	2 retrocopies	retro_ttru_1534, retro_ttru_433,
Drosophila melanogaster	FBgn0031145	1 retrocopy	retro_dmel_27,