RetrogeneDB ID: retro_cpor_1411

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:1475194..1475737(-)
• Located in intron of: ENSCPOG00000011675

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCTS1
• Ensembl ID: ENSCPOG00000005502
• Aliases: None
• Description: None

Sequence

>retro_cpor_1411
ATGTTCAAGAAATTTGACGAAAAGGAAAATGTGTCCAATTGCATCCAGTTGAAAACTTCAGTTATAAAGGGTATGAAGAA
CCAACTGATAGAGCAGTTTCCAGATATTGAGCCATGGCTTAACCAAATCATGCCTAAGAAAGAGCCTGTCAAAATGGTCC
GATGCCATGAACATACGGAAATCCTTACGGTAAATGGAGAATTAATTTTTTTTAGACAAAGGAAAGGACCTTTTTATCCA
ACTCTAAGGTTACTTCACAAATACCCTTTTATCCTGCCACACCAGCAAGTTGATAAAGGAGCCATCAAATTTGTGCTAAG
CGGTGCGAATATCATGTGCCCAGGTTTAACTTCTCCAGGAGCAAAGCTTTACCCTGCCGCAGTCGATACGATTGTTGCAG
TCATGGCGGAAGGAAAACAGCACGCGCTGTGTATTGGAGTCATGAAGATGTCTGGAGGAGACATTGGGAAAATTAACAAA
GGAATCGGCATTGAGAATATCCATTATTTAAATGATGGGCTGTGGCACATGAAGACATATAAA

Alignment

ORF - retro_cpor_1411 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF
          MFKKFDEKENVSNCIQLKTSVIKG.KNQLIEQFP.IEPWLNQIMPKK.PVK.VRCHEH.EILTVNGEL..
Retrocopy MFKKFDEKENVSNCIQLKTSVIKGMKNQLIEQFPDIEPWLNQIMPKKEPVKMVRCHEHTEILTVNGELXX

Parental  FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAADTIVAIMAEGKQ
          .RQR.GPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAA.DTIVA.MAEGKQ
Retrocopy XRQRKGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAVMAEGKQ

Parental  HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK
          HALC.GVMKMS..DI.K.NKGIGIENIHYLNDGLWHMKTYK
Retrocopy HALCIGVMKMSGGDIGKINKGIGIENIHYLNDGLWHMKTYK

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	5.35 RPM	14.49 RPM
SRP017611_kidney	4.19 RPM	11.41 RPM
SRP017611_liver	1.96 RPM	13.67 RPM
SRP040447_lung	5.57 RPM	8.98 RPM
SRP040447_skeletal_muscle	1.22 RPM	7.92 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1411 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1411 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 23 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034992	1 retrocopy	retro_btau_116,
Canis familiaris	ENSCAFG00000018545	1 retrocopy	retro_cfam_94,
Cavia porcellus	ENSCPOG00000005502	1 retrocopy	retro_cpor_1411 ,
Equus caballus	ENSECAG00000014597	1 retrocopy	retro_ecab_697,
Erinaceus europaeus	ENSEEUG00000007258	1 retrocopy	retro_eeur_197,
Echinops telfairi	ENSETEG00000015462	1 retrocopy	retro_etel_19,
Homo sapiens	ENSG00000232119	1 retrocopy	retro_hsap_2422,
Gorilla gorilla	ENSGGOG00000009420	1 retrocopy	retro_ggor_1507,
Myotis lucifugus	ENSMLUG00000015101	1 retrocopy	retro_mluc_16,
Macaca mulatta	ENSMMUG00000009043	1 retrocopy	retro_mmul_626,
Monodelphis domestica	ENSMODG00000010354	1 retrocopy	retro_mdom_203,
Mustela putorius furo	ENSMPUG00000001407	1 retrocopy	retro_mputfur_98,
Mus musculus	ENSMUSG00000000355	3 retrocopies	retro_mmus_2504, retro_mmus_2505, retro_mmus_69,
Nomascus leucogenys	ENSNLEG00000015021	1 retrocopy	retro_nleu_2442,
Oryctolagus cuniculus	ENSOCUG00000014315	1 retrocopy	retro_ocun_212,
Pan troglodytes	ENSPTRG00000022241	1 retrocopy	retro_ptro_1396,
Pteropus vampyrus	ENSPVAG00000013249	3 retrocopies	retro_pvam_1323, retro_pvam_645, retro_pvam_867,
Rattus norvegicus	ENSRNOG00000002563	2 retrocopies	retro_rnor_1841, retro_rnor_957,
Ictidomys tridecemlineatus	ENSSTOG00000011496	2 retrocopies	retro_itri_1136, retro_itri_1468,
Tupaia belangeri	ENSTBEG00000010666	2 retrocopies	retro_tbel_1485, retro_tbel_4265,
Tarsius syrichta	ENSTSYG00000001440	1 retrocopy	retro_tsyr_55,
Tursiops truncatus	ENSTTRG00000007208	1 retrocopy	retro_ttru_1587,
Vicugna pacos	ENSVPAG00000001801	1 retrocopy	retro_vpac_138,