RetrogeneDB ID: retro_tsyr_1000

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_271187:2753..3205(-)
• 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_1000
TCTGTGCTTCTGGACCTGCTCAGTACAGATGGGGAGGCCAGGCCAGAAAGTTAGGAAAGAGCTGTGTCTGCCCCAGCCAA
TGTGACCTTGGAAAAGGATTGCAAGCAGCCCTGACTCTAGCAAAAGAAAAGTTTGACTGTGTGGATGTGGCTATCAACCG
TATAGGCATTGTAGTGACCATCAAGACTACAACTTAAAGAAGAGCCAGGCTGATACCTCGGAGAACTTCCAGTGAGTTCT
TAATGTGAATCTCTTAGGGATCTTCAGTGTGGTCCACCTTGTGGCTGGTGAGATGGGCCAGAATGAACCAGATCAGGGAG
GCCAACATGGGGTCATTATCAACACCGCCAGTGTGGCTACCTTTGAGGGCCAGGCTGAACAAGCTGCATATTTTGCTTCC
AGGGGAGGCATAGTGAGCATGAAACTGCCCATTGCTTGGGGATCTATCTCCC

Alignment

ORF - retro_tsyr_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.03 %
• Parental protein coverage: 58.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVLLDLPNSGGEAQAKKFGKSCVFAPADVTSEKD-VQAALTLAKEKFGRVDVAVNCAGIAVAIKT-YNLK
          .VLLDL....GEA.........V.APA.VT.EKD..QAALTLAKEKF..VDVA.N..GI.V.IKT.YNLK
Retrocopy SVLLDLLSTDGEARPES*ERA-VSAPANVTLEKD<LQAALTLAKEKFDCVDVAINRIGIVVTIKT<YNLK

Parental  KSQAHTLDDFQRVLNVNLLGTFNMIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGG
          KSQA.T...FQ.VLNVNLLG.F....LVAGEMGQNEPDQGGQ.GVIINTASVA.FEGQ..QAAY.AS.GG
Retrocopy KSQADTSENFQ*VLNVNLLGIFSVVHLVAGEMGQNEPDQGGQHGVIINTASVATFEGQAEQAAYFASRGG

Parental  IVGMTLPIA-RDLAP
          IV.M.LPIA..DL.P
Retrocopy IVSMKLPIA>GDLSP

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_1000 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,