RetrogeneDB ID: retro_cpor_181

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:56203461..56203921(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT2
• Ensembl ID: ENSCPOG00000000419
• Aliases: None
• Description: None

Sequence

>retro_cpor_181
GCAGCGCTCAGAGCCATAGCCGCCACGGGGTGCAGGGGGCACAGGGGGCACAGGGCCACAGGTGTGACTGATGGGGATGA
AGTGGCCAAGGCCCAGCAGGCAGCTCCTGGAAAAGCAGCCCCAACAACCTCCTCCCGGATCCTGGACAGAAGCCTCCCAG
CTGCCATTTATATAAGGAGCAGCAGTATCTCGTGTTCCGTGATGAGCCCCCACCCCACCAGGCTTCTGTGCATTTCCTGG
TTATTCCTAAGAAGCCCATTCCTTGCATTAGTCAGGCTGAGGAAGAAGACCAGCAGATTGTAGCACACCTCCTCCTCCTT
GTGGCCATGAAGAAGCAAAGGCCGAGGGCCTGGGCGATGAATACTGACTTGTGGTCATTGATAGAAAGCAGGACACACAA
TCTGTATATCACTTGCACATTCACATCCTTGGAGGCTGCCAGCGCCAGTGGTCTCCAGGT

Alignment

ORF - retro_cpor_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.31 %
• Parental protein coverage: 92.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVHRALAAAGARRLQVRGAAGMTDGNEVAKAQQAAPGGASPTIFSRILDRSLPADI-LHEDQQCLVFRDV
          A..RA.AA.G..........G.TDG.EVAKAQQAAPG.A.PT..SRILDRSLPA.I.L...QQ.LVFRD.
Retrocopy AALRAIAATGXXXXXXXXXTGVTDGDEVAKAQQAAPGKAAPTTSSRILDRSLPAAI<LYKEQQYLVFRDE

Parental  AP--QAPVHFLVIPKKPIPRISQAEEEDQQLLGH-LLLVAKK-IAKAEGLGDGYRLVINDGKLGAQSVYH
          .P..QA.VHFLVIPKKPIP.ISQAEEEDQQ...H.LLLVA.K..AKAEGLGD.Y.LV..D.K...QSVYH
Retrocopy PPPHQASVHFLVIPKKPIPCISQAEEEDQQIVAHLLLLVAMK<EAKAEGLGDEY*LVVIDRKQDTQSVYH

Parental  LHIHVLGGRQLQWPPG
          LHIH.LGG.Q.QW.PG
Retrocopy LHIHILGGCQRQWSPG

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	17.14 RPM
SRP017611_kidney	0.00 RPM	98.51 RPM
SRP017611_liver	0.00 RPM	49.93 RPM
SRP040447_lung	0.00 RPM	37.68 RPM
SRP040447_skeletal_muscle	0.00 RPM	31.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_181 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_181 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011444	1 retrocopy	retro_btau_1129,
Callithrix jacchus	ENSCJAG00000010068	1 retrocopy	retro_cjac_1343,
Cavia porcellus	ENSCPOG00000000419	1 retrocopy	retro_cpor_181 ,
Dasypus novemcinctus	ENSDNOG00000009083	2 retrocopies	retro_dnov_201, retro_dnov_854,
Echinops telfairi	ENSETEG00000017929	1 retrocopy	retro_etel_486,
Homo sapiens	ENSG00000137133	1 retrocopy	retro_hsap_2603,
Gorilla gorilla	ENSGGOG00000011265	1 retrocopy	retro_ggor_1823,
Loxodonta africana	ENSLAFG00000015022	1 retrocopy	retro_lafr_737,
Macaca mulatta	ENSMMUG00000016337	1 retrocopy	retro_mmul_1509,
Nomascus leucogenys	ENSNLEG00000026914	1 retrocopy	retro_nleu_1534,
Oryctolagus cuniculus	ENSOCUG00000027206	1 retrocopy	retro_ocun_66,
Otolemur garnettii	ENSOGAG00000011830	1 retrocopy	retro_ogar_765,
Pongo abelii	ENSPPYG00000019082	1 retrocopy	retro_pabe_2310,
Pan troglodytes	ENSPTRG00000020923	1 retrocopy	retro_ptro_1754,
Pteropus vampyrus	ENSPVAG00000003028	1 retrocopy	retro_pvam_842,
Tupaia belangeri	ENSTBEG00000013020	1 retrocopy	retro_tbel_4676,
Tarsius syrichta	ENSTSYG00000002700	7 retrocopies	retro_tsyr_1210, retro_tsyr_1356, retro_tsyr_1483, retro_tsyr_1485, retro_tsyr_311, retro_tsyr_468, retro_tsyr_48,
Tursiops truncatus	ENSTTRG00000011932	1 retrocopy	retro_ttru_1302,