RetrogeneDB ID: retro_tsyr_1965

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_72919:4789..5740(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSTSYG00000014394
• Aliases: None
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_tsyr_1965
ACCCAGCAGGGCTGTGGTATCCATGCCATAGAGCTGAATCCATCTAGAACACTGCTAGCCATTGGAGGAGACAACCCTAA
CAGTCTTGCCATCTATGGACTGCCTACACTAGATCCTGTGTGTGTGGGAGATGATGGACACAAGGACTGGATCTTTTCCA
TTGCATGGATCAATGACACCATGGCTGTATTTGGTTCATGTCATGGTTCTATGGGACTCTGGGAAGAGACAGATGATGTG
TTGACCCAAAGTGTTGCAAGACACAATGTGTCACGGGTTCCTGTGTATGCACACATCACTCACAAGGCCTTAAAGGATAT
CCCCAAGGAGGAAACAAACCCTGATAACTGCAAGGTCCGGGCCCTAGCCTTCAATAACAAGAACAAGGAATTGGGAGCAG
TATCTTTGGATGGCTACTTTCATCTCTGGAAAGCTGAAAATACACCGGCTAAGCTCCTCTCTACCAAACTGACATATTGC
CGTGAGAATGTGTATCTAGCCTATGGTAGTGAATGGTCAGTGTATGCAGTGGGCTCCCAAGCTCATGTCTCCTTCTTGGA
TGCACGGCAGCCATCATACAACGTCAAGTCTGTCTGCTCCAGGGAGTGAGGCAGTGGAATCCGGTCAGTGAGTTTCTATG
AGCACATCATCACTGTGGGAACAGGGGCAGGGCTACCTGCTGTTTTATGACATCCGAGCTCAGAGATTTCTGGAAGAGAG
GCTCTCAGCTTGTAATGGGTCCAAGCCCAGACTAGCAGGGGAGAATCTGAACTAACCACTGGCAAAGGCTGGCTGAATCA
TGATGAAACCTGGAGAAATTACTTTTCGGACATTGATTTCTTCCCCAATGCTGTTTACATGCACTGCTATGACTCGTTTG
GGACGAAACTCTTTGTGGCAGGAGGTCCCCTCCCTTCAGGGCTCCATGGAAACTATGCTGGCCTCTGGAGT

Alignment

ORF - retro_tsyr_1965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.42 %
• Parental protein coverage: 69.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGDDGHKDWIFSIAWINDTMAVSGSRDGS
          TQQGCGIHAIELNPSRTLLA.GGDNPNSLAIY.LPTLDPVCVGDDGHKDWIFSIAWINDTMAV.GS..GS
Retrocopy TQQGCGIHAIELNPSRTLLAIGGDNPNSLAIYGLPTLDPVCVGDDGHKDWIFSIAWINDTMAVFGSCHGS

Parental  MGLWEVTDDVLTKSDARHNVSRVPMYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYF
          MGLWE.TDDVLT.S.ARHNVSRVP.YAHITHKALKDIPKE.TNPDNCKVRALAFNNKNKELGAVSLDGYF
Retrocopy MGLWEETDDVLTQSVARHNVSRVPVYAHITHKALKDIPKEETNPDNCKVRALAFNNKNKELGAVSLDGYF

Parental  HLWKAENTLAKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIRSV
          HLWKAENT.AKLLSTKL.YCRENV.LAYGSEWSVYAVGSQAHVSFLD.RQPSYNVKSVCSRE.GSGIRSV
Retrocopy HLWKAENTPAKLLSTKLTYCRENVYLAYGSEWSVYAVGSQAHVSFLDARQPSYNVKSVCSRE*GSGIRSV

Parental  SFYEHIITVGT-GQGSLLFYDIRAQRFLEERLSACNGSKPRLAGENL-KLTTGKGWLNHDETWRNYFSDI
          SFYEHIITVGT.GQG.LLFYDIRAQRFLEERLSACNGSKPRLAGENL..LTTGKGWLNHDETWRNYFSDI
Retrocopy SFYEHIITVGT>GQGYLLFYDIRAQRFLEERLSACNGSKPRLAGENL<ELTTGKGWLNHDETWRNYFSDI

Parental  DFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
          DFFPNAVY.HCYDS.GTKLFVAGGPLPSGLHGNYAGLWS
Retrocopy DFFPNAVYMHCYDSFGTKLFVAGGPLPSGLHGNYAGLWS

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_1965 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178, retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965 ,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,