RetrogeneDB ID: retro_tsyr_1542

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_484417:531..1028(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B10
• Ensembl ID: ENSTSYG00000005340
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:HGNC Symbol;Acc:4800]

Sequence

>retro_tsyr_1542
AACATGAAGGGTCTGGTCACAGTTATACCCAGAGGAGACTCAGACCCGGGCCTGGCCTTGGTGGAGCGACTGGTAAGGCA
GGGGGCTGCTGCTGTGCTTCTGGACCAGCCCAACTCAGGTAGGGAGGCCCAGGCCAAGAAGTTTGGAAAGAGCTGCATCT
GCCCTAGCTGACGTGACCTCTGAGAAAGATGTGCAAGCAGCTCTGACTCTAACAAAAGAAAAATTTGGCTGTGCAGATGT
GCCTGTCAACTGTGCAGACATTGCAGTGGCCATCAAGACATACAACTTAAAGAAGAGCCAGGCTCATACCTTGGAGAACT
TCTAGCGCGTTCTCAATGTGAATCTCATAGGCGCCTTTACTATGATCCCACTTGGTAGCTGGTGAGATGGACCAGAAAGA
ACCAGACCAGGGAGGCCAACATGGGGTCATCCTCAACACTGCCAGTGTAGCTGCCTTTGAGAGCCAGGTTAGACAAGTTG
CATACTCTATTTCCAAG

Alignment

ORF - retro_tsyr_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVQGLVAVITGGASGLGLATVERLVRQGAAAVLLDL-PNSGGEAQAKKFGKSCVFAPADVTSEKDVQAAL
          N..GLV.VI..G.S..GLA.VERLVRQGAAAVLLD..P...G.............A.ADVTSEKDVQAAL
Retrocopy NMKGLVTVIPRGDSDPGLALVERLVRQGAAAVLLDQ>PTQVGRPRPRSLERAAS-ALADVTSEKDVQAAL

Parental  TLAKEKFGRVDVAVNCAGIAVAIKTYNLKKSQAHTLDDFQRVLNVNLLGTFNMI-RLVAGEMGQNEPDQG
          TL.KEKFG..DV.VNCA.IAVAIKTYNLKKSQAHTL..F.RVLNVNL.G.F.MI..LVAGEM.Q.EPDQG
Retrocopy TLTKEKFGCADVPVNCADIAVAIKTYNLKKSQAHTLENF*RVLNVNLIGAFTMI>HLVAGEMDQKEPDQG

Parental  GQRGVIINTASVAAFEGQVGQAAYSASK
          GQ.GVI.NTASVAAFE.QV.Q.AYS.SK
Retrocopy GQHGVILNTASVAAFESQVRQVAYSISK

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1542 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542 , retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,