RetrogeneDB ID: retro_cpor_1059

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_42:3345985..3346386(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSCPOG00000004707
• Aliases: None
• Description: Histone H3 [Source:UniProtKB/TrEMBL;Acc:H0V3S0]

Sequence

>retro_cpor_1059
ATGGCTCGAACTAAGCAGACTGCATGTAAGTCCACTGGTGGGAAAGCCCCCCAAAACAGCTGGCCACTAAAGCTGCCAGG
AAAAGCGCTCCCTCTATTGGCCCGGGTGAAGAAGCCTCATTGCTACAGGCCTGGAACCATAGCACTTTGAGAGATTGGCT
GCTACCAGAAGTTAACTGAACTGCTCATTGGGAAGCTACCTTTCAGAGGTTGGTGAGAGAGATTGCCCAGGATTTCAAGA
CCAACTTGAGGTTTCAGAGTGCACCTATTGGTGCTCTTCAGGAGGCTAGTGAAGCATACCTGGTGGGCTTATTTGAAGAT
ACTAATCTGTGTGCCATCCACACTAAGACAGTCACCACCATGCCCAAAGACAGCCAGTTGGGGCCAAAACGGGGAGAGAG
A

Alignment

ORF - retro_cpor_1059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.61 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPR-KQLATKAARKSAPSTGG-VKKPHRYRPGTVALREIRRYQKSTELLIRKLPF
          MARTKQTA.KSTGGKAP..KQLATKAARKSAPS.G..VKKPH.YRPGT.AL.EI..YQK.TELLI.KLPF
Retrocopy MARTKQTACKSTGGKAPQ<KQLATKAARKSAPSIGP>VKKPHCYRPGTIAL*EIGCYQKLTELLIGKLPF

Parental  -QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
          .QRLVREIAQDFKT.LRFQSA.IGALQEASEAYLVGLFEDTNLCAIH.K.VT.MPKD.QL....RGER
Retrocopy <QRLVREIAQDFKTNLRFQSAPIGALQEASEAYLVGLFEDTNLCAIHTKTVTTMPKDSQLGPK-RGER

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	67.75 RPM
SRP017611_kidney	0.00 RPM	163.52 RPM
SRP017611_liver	0.00 RPM	79.74 RPM
SRP040447_lung	0.00 RPM	205.10 RPM
SRP040447_skeletal_muscle	0.00 RPM	127.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1059 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1059 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 10 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009765	3 retrocopies	retro_amel_1636, retro_amel_1794, retro_amel_192,
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Cavia porcellus	ENSCPOG00000004707	7 retrocopies	retro_cpor_1059 , retro_cpor_1390, retro_cpor_1524, retro_cpor_432, retro_cpor_695, retro_cpor_842, retro_cpor_853,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139, retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,