RetrogeneDB ID: retro_itri_1099

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393376.1:653620..654277(+)
• Located in intron of: ENSSTOG00000016462

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B12
• Ensembl ID: ENSSTOG00000005473
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 12 [Source:HGNC Symbol;Acc:18646]

Sequence

>retro_itri_1099
ATAAAAGAAAAATTCAAAGTGGAGACAAGGACCATTGCTGTTGACTTTACATCAGAAGATATTTATGATAAAATTAAAAC
AGACCTGGCGGGTCTTGAAATTGGCATTTTAGTGAACAATGTGGGAATCTCATATGAGTATCCTGAATACTTTTTGGAAA
TTCCTGACTTGGACAATGCCATTAGGAAACTGATAAATATTAATATTCTTTCTGTTTGTAAGATGACATGAGTGGTGCTG
CCTGGCATGGTAGAAAGGTCTAAAGGTGCAATTCTGAACATCTCCTCTGCCAGTGGCATGTTTCCGGTTCCACTATTGGC
CATCTACTCTGCGACCAAGGCTTTTGTAGATTTCTTCTCTCAGTACCTCCATGAGGAGTATAGAAGCAAGGGCATCTTTG
TGCAGAATGTCCTGCCATTTTACATAGCTACAAAACTGGCTAAAATCCGAAAGCCAACTTGGGACAAGCCCTCTTCAGAG
ACATTTGTGAAATCTGCAATTAAAACAGTAGGCTTGCAGTCCCGAACCAATGGATACCTGATCCATTCTCTTATGGGCTC
AATAATCTCCATCCTGCCTTCTTGGATTTACCTTAAAATATCCATGGGTCTCAACAAGTCTCTGAGGGCTCGCTATCTGA
AGAAAGCCAAGAAGAAC

Alignment

ORF - retro_itri_1099 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEEKFKVETRTIAVDFTSEDIYDKIKTDLAGLEIGILVNNVGISYEYPEYFLEIPDLDNAIKKLINVNIL
          ..EKFKVETRTIAVDFTSEDIYDKIKTDLAGLEIGILVNNVGISYEYPEYFLEIPDLDNAI.KLIN.NIL
Retrocopy IKEKFKVETRTIAVDFTSEDIYDKIKTDLAGLEIGILVNNVGISYEYPEYFLEIPDLDNAIRKLININIL

Parental  SVCKMTRVVLPGMVERSKGAILNISSASGVFPVPLLAIYSATKAFVDFFSQCLHEEYRSKGIFVQSVLPF
          SVCKMT.VVLPGMVERSKGAILNISSASG.FPVPLLAIYSATKAFVDFFSQ.LHEEYRSKGIFVQ.VLPF
Retrocopy SVCKMT*VVLPGMVERSKGAILNISSASGMFPVPLLAIYSATKAFVDFFSQYLHEEYRSKGIFVQNVLPF

Parental  YVATKLAKIRKPTWDKPSSETFVKSAVKTVGLQSRTNGYLIHSLMGSIISILPSWIYLKISMGLNKSVRA
          Y.ATKLAKIRKPTWDKPSSETFVKSA.KTVGLQSRTNGYLIHSLMGSIISILPSWIYLKISMGLNKS.RA
Retrocopy YIATKLAKIRKPTWDKPSSETFVKSAIKTVGLQSRTNGYLIHSLMGSIISILPSWIYLKISMGLNKSLRA

Parental  RYLKKAKKN
          RYLKKAKKN
Retrocopy RYLKKAKKN

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_1099 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1099 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011325	1 retrocopy	retro_cjac_2489,
Dipodomys ordii	ENSDORG00000004834	1 retrocopy	retro_dord_561,
Homo sapiens	ENSG00000149084	1 retrocopy	retro_hsap_3684,
Gorilla gorilla	ENSGGOG00000002003	1 retrocopy	retro_ggor_2491,
Nomascus leucogenys	ENSNLEG00000017959	1 retrocopy	retro_nleu_2273,
Oryctolagus cuniculus	ENSOCUG00000016351	1 retrocopy	retro_ocun_1335,
Otolemur garnettii	ENSOGAG00000009102	1 retrocopy	retro_ogar_3391,
Pongo abelii	ENSPPYG00000003343	1 retrocopy	retro_pabe_3021,
Pan troglodytes	ENSPTRG00000003522	1 retrocopy	retro_ptro_2499,
Ictidomys tridecemlineatus	ENSSTOG00000005473	1 retrocopy	retro_itri_1099 ,
Tursiops truncatus	ENSTTRG00000005103	1 retrocopy	retro_ttru_772,