RetrogeneDB ID: retro_cpor_1249

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:24020547..24021163(-)
• Located in intron of: ENSCPOG00000009162

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000002962
• Aliases: None
• Description: None

Sequence

>retro_cpor_1249
ATGGCAGCCGCTAAGGATACTCATGAGGACCATGATACCTCCACTGAGAATGCAGACGAGTCCAACCATGATCCCCAGTT
TGAACCAATAGTTTCTCTTCCCGAGCAAGAAATTAAAACACTGGAGGAAGATGAGGAAGAACTTTTTAAAATGCGAGCAA
AGTTGTTCCGATTTGCTTCAGAGAATGATAGCCCAGAGTGGAAGGAATGTGGCACTGGTGACGTCAAACTCCTAAAGCAT
AAGGATAAGGGGACCATTCGCCTCCTCATGAGGAGGGACAAGACCCTGAAGATCTGCGCCAACCACTATATCTAGCCCAT
GATGGAGCTTAAGCCAAATGCTGGTAGTGACCGTGCCTGGGTCTGGAATACCCATGCTGACTTTGTCGATGAGTACCCCA
CGCCGGAGCTGCTTGCCATCCGCTTCCTAAATGCTGAAAATGCACAAAAATTTAAAACAAAGTTTGAAGAATGCAGGAAA
GAGATTGAAGAGAGAAAAAAAAAAAGGACTGGGCAAAAATGATAATGCGGAAAAAGTAGCTGAAAAGCTAGAAGCTCTGT
CTGTAAAGGAGAATAAGGACCCTGGAAAAGAGACCAAAGAGAAATCAGAGAAGCAA

Alignment

ORF - retro_cpor_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAKDTHEDHDTSTENADESNHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDSPEWKER
          MAAAKDTHEDHDTSTENADESNHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDSPEWKE.
Retrocopy MAAAKDTHEDHDTSTENADESNHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDSPEWKEC

Parental  GTGDVKLLKHKDKGTIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADEYPKPELLAI
          GTGDVKLLKHKDKGTIRLLMRRDKTLKICANHYI.PMMELKPNAGSDRAWVWNTHADF.DEYP.PELLAI
Retrocopy GTGDVKLLKHKDKGTIRLLMRRDKTLKICANHYI*PMMELKPNAGSDRAWVWNTHADFVDEYPTPELLAI

Parental  RFLNAENAQKFKTKFEECRKEIEE-RPPAGLGKNDNAEKVAEKLEALSVKENKDPGKETEEKSEKQ
          RFLNAENAQKFKTKFEECRKEIEE.....GLGKNDNAEKVAEKLEALSVKENKDPGKET.EKSEKQ
Retrocopy RFLNAENAQKFKTKFEECRKEIEE>XXXXGLGKNDNAEKVAEKLEALSVKENKDPGKETKEKSEKQ

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	0.35 RPM	16.97 RPM
SRP017611_kidney	0.42 RPM	18.01 RPM
SRP017611_liver	0.52 RPM	9.31 RPM
SRP040447_lung	0.25 RPM	23.88 RPM
SRP040447_skeletal_muscle	0.18 RPM	10.04 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1249 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1249 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 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010749	1 retrocopy	retro_cjac_2619,
Cavia porcellus	ENSCPOG00000002962	1 retrocopy	retro_cpor_1249 ,
Dipodomys ordii	ENSDORG00000011317	2 retrocopies	retro_dord_241, retro_dord_602,
Echinops telfairi	ENSETEG00000015996	2 retrocopies	retro_etel_1018, retro_etel_1518,
Homo sapiens	ENSG00000099901	2 retrocopies	retro_hsap_1727, retro_hsap_4797,
Gorilla gorilla	ENSGGOG00000000784	1 retrocopy	retro_ggor_170,
Macropus eugenii	ENSMEUG00000016620	8 retrocopies	retro_meug_1064, retro_meug_1553, retro_meug_1670, retro_meug_1795, retro_meug_272, retro_meug_422, retro_meug_657, retro_meug_753,
Myotis lucifugus	ENSMLUG00000017535	1 retrocopy	retro_mluc_1429,
Macaca mulatta	ENSMMUG00000020100	1 retrocopy	retro_mmul_1215,
Monodelphis domestica	ENSMODG00000010312	5 retrocopies	retro_mdom_1290, retro_mdom_1397, retro_mdom_1406, retro_mdom_1996, retro_mdom_288,
Mus musculus	ENSMUSG00000005732	1 retrocopy	retro_mmus_3632,
Nomascus leucogenys	ENSNLEG00000005684	2 retrocopies	retro_nleu_2991, retro_nleu_934,
Otolemur garnettii	ENSOGAG00000034333	2 retrocopies	retro_ogar_1428, retro_ogar_2735,
Pongo abelii	ENSPPYG00000011593	4 retrocopies	retro_pabe_1438, retro_pabe_1470, retro_pabe_3731, retro_pabe_943,
Rattus norvegicus	ENSRNOG00000001884	4 retrocopies	retro_rnor_1817, retro_rnor_811, retro_rnor_884, retro_rnor_907,
Sarcophilus harrisii	ENSSHAG00000006873	1 retrocopy	retro_shar_9,
Ictidomys tridecemlineatus	ENSSTOG00000026840	2 retrocopies	retro_itri_1579, retro_itri_345,
Tarsius syrichta	ENSTSYG00000013573	1 retrocopy	retro_tsyr_320,
Tursiops truncatus	ENSTTRG00000008142	2 retrocopies	retro_ttru_456, retro_ttru_890,