RetrogeneDB ID: retro_tsyr_2178

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_99642:4683..5350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSTSYG00000000666
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 2 [Source:HGNC Symbol;Acc:9548]

Sequence

>retro_tsyr_2178
TTGATTATCTTTGGTCCACCTGGTACAGGCAAGACACTTTGTGCTCGGGCAGTTGCTAATAGGACTGATGCTTACTTCAT
TCGAGTTATTGGATCTGAGCTTGTACAGAAATATGTTGGTGAGGGGGCTCGAATGGTTTGTGAACTCTTTGAAATGGCCA
GAACAAAAAAAAACCTGCCTTATCTTCTTTGATGAAATTGATGCTATTGGAGGGGCTCGGTTTGATGATGGTGCTGGAGG
TGACAATGAAGTGCAGAGAACAATGTTGGAACTGATCTATCAGCTGGATGGTTTTGATCCTCGAGGCAATATTAAAGTGC
TGATGGCTACTAACAAACCTGATACTTTGGATCCAGCACTGATGAGGCCAGGGAGATTGGACAGAAAGATTGAATTTAGC
TTACCTGATCTAGAGGGTAGGACTCACATCTTTAAGATTCATGCCCGTTCAATGAGTGTTGAAAGAGATATCAGATTTGA
ATTGTTAGCACGGCTGTGTCCAAATAGTACTGGTGCTGAAATTAGAAGCATCTGTACAGAAGCTGGCATGTTTGCCATCA
GAGCATGGTGAAAAATTGCTACTGAAAAGAATTTCTTGGAAGCTGTAAATGAGGTCATTAAGTCTTATGCCAAATTCAGT
GCTACTCCCTGCTACATGACATACAAC

Alignment

ORF - retro_tsyr_2178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.93 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLLFGPPGTGKTLCARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKA-CLIFFDEIDAI
          ...FGPPGTGKTLCARAVANRTDA.FIRVIGSELVQKYVGEGARMV.ELFEMAR.....CLIFFDEIDAI
Retrocopy LIIFGPPGTGKTLCARAVANRTDAYFIRVIGSELVQKYVGEGARMVCELFEMARXXXX>CLIFFDEIDAI

Parental  GGARFDDGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEG
          GGARFDDGAGGDNEVQRTMLELI.QLDGFDPRGNIKVLMATN.PDTLDPALMRPGRLDRKIEFSLPDLEG
Retrocopy GGARFDDGAGGDNEVQRTMLELIYQLDGFDPRGNIKVLMATNKPDTLDPALMRPGRLDRKIEFSLPDLEG

Parental  RTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSY
          RTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRS.CTEAGMFAIRA..KIATEK.FLEAVN.VIKSY
Retrocopy RTHIFKIHARSMSVERDIRFELLARLCPNSTGAEIRSICTEAGMFAIRAW*KIATEKNFLEAVNEVIKSY

Parental  AKFSATPRYMTYN
          AKFSATP.YMTYN
Retrocopy AKFSATPCYMTYN

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_2178 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257, retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178 ,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,