RetrogeneDB ID: retro_itri_435

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393291.1:4501067..4501315(-)
• Located in intron of: ENSSTOG00000010385

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2
• Ensembl ID: ENSSTOG00000002536
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 2 (liver) [Source:HGNC Symbol;Acc:2288]

Sequence

>retro_itri_435
ATGCTATAGAATCTGCTGGGTTTTTGTCAGCTTGCCCAAAGGACCATCAGCACTGATTCAATAGACATTTTGAAAATAAA
GTTCCTGAGAAACAAAAGCAGTTTCAGGAGGATAATGGAATTCCAGTGCATCTAAAGAGCTGAGCGGCTGATGCCCTTCT
TTATAGGGACACCATGATTCTTACAGTTGGTGGAACAGCATATGTCATATAGGAGTTGGCTGTGGCTTCATCTCCCAAAT
GGCAGGAT

Alignment

ORF - retro_itri_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLRNLLRFRQIAQRTISTAS-RRHFENKVPEKQKLFQEDNGIPVHLKGGVADALLYRATMVLTVGGTAYA
          ML.NLL.F.Q.AQRTIST.S..RHFENKVPEKQK.FQEDNGIPVHLK...ADALLYR.TM.LTVGGTAY.
Retrocopy ML*NLLGFCQLAQRTISTDS<NRHFENKVPEKQKQFQEDNGIPVHLKS*AADALLYRDTMILTVGGTAYV

Parental  IYELAKASFPKKQD
          I.ELA.AS.PK.QD
Retrocopy I*ELAVASSPKWQD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_435 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_435 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014453	1 retrocopy	retro_amel_723,
Bos taurus	ENSBTAG00000005096	6 retrocopies	retro_btau_1071, retro_btau_1230, retro_btau_1436, retro_btau_1469, retro_btau_1703, retro_btau_507,
Callithrix jacchus	ENSCJAG00000010305	2 retrocopies	retro_cjac_1523, retro_cjac_4129,
Cavia porcellus	ENSCPOG00000007404	2 retrocopies	retro_cpor_1300, retro_cpor_527,
Dipodomys ordii	ENSDORG00000015425	2 retrocopies	retro_dord_701, retro_dord_790,
Homo sapiens	ENSG00000112695	2 retrocopies	retro_hsap_1434, retro_hsap_2961,
Gorilla gorilla	ENSGGOG00000005865	2 retrocopies	retro_ggor_1104, retro_ggor_2051,
Loxodonta africana	ENSLAFG00000002313	1 retrocopy	retro_lafr_811,
Microcebus murinus	ENSMICG00000015747	3 retrocopies	retro_mmur_381, retro_mmur_548, retro_mmur_799,
Nomascus leucogenys	ENSNLEG00000004949	2 retrocopies	retro_nleu_1412, retro_nleu_735,
Pongo abelii	ENSPPYG00000016781	2 retrocopies	retro_pabe_1187, retro_pabe_2456,
Pteropus vampyrus	ENSPVAG00000010401	6 retrocopies	retro_pvam_1144, retro_pvam_1408, retro_pvam_443, retro_pvam_57, retro_pvam_656, retro_pvam_741,
Rattus norvegicus	ENSRNOG00000042903	1 retrocopy	retro_rnor_52,
Sus scrofa	ENSSSCG00000004480	1 retrocopy	retro_sscr_296,
Ictidomys tridecemlineatus	ENSSTOG00000002536	5 retrocopies	retro_itri_435 , retro_itri_464, retro_itri_608, retro_itri_890, retro_itri_892,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,
Tupaia belangeri	ENSTBEG00000007294	7 retrocopies	retro_tbel_1177, retro_tbel_178, retro_tbel_3617, retro_tbel_4102, retro_tbel_4330, retro_tbel_738, retro_tbel_781,
Tursiops truncatus	ENSTTRG00000007874	1 retrocopy	retro_ttru_669,