RetrogeneDB ID: retro_tsyr_1807

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_59740:2039..2555(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSTSYG00000010674
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_tsyr_1807
ATGGTGGCCACCTTAGTAGCTTCTCGGGGAGTGGGGCCAGCACCAGCTTGAGGACCAGGAGCCATCGCTCCAGACTGGGA
AAACCAGGAAGCGTCCACAGGGACCACTATCATGGCTGTGCAATTTGACTGGAGTGTGGTTCTGGGGACCGACCCCAGAA
CAACCACTGGGTCCTACATTGCCAGTCACGTGACCGACAAGTTGACCCCTATTCACGACCACATTTTCTGCTGCTGCTTG
GGCTCAGCAGCTGATACCCAGGCAGTAGCTGATGCTGTCACTTAGCTTGGTTTTCACAGCATTGCACTGAATGAGCTTCC
ACTGGTACACACAGCAGCCAGCCTCCTTAAGGAGATGTGTTACCAATACTGAGTCAACCTCATGGCAGGAATCATCGTCG
CAGGCTGGAACCCTCAAGAAGGTGGGCAGATGTACTCAGCGCCCATGGGTGATATGATGGTAAGGCAGTCTTTTGCCATT
AGAGGCTCTGGGAGTTCCTATATATATGGCTGTGTG

Alignment

ORF - retro_tsyr_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.02 %
• Parental protein coverage: 72.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAATLVAARGVGPAPAWRPEAIAPDWETREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANQVTDKLTP
          M.ATLVA.RGVGPAPA..P.AIAPDWE..E.STGTTIMAVQFD..VVLG.D.RTTTGSYIA..VTDKLTP
Retrocopy MVATLVASRGVGPAPA*GPGAIAPDWENQEASTGTTIMAVQFDWSVVLGTDPRTTTGSYIASHVTDKLTP

Parental  IHDHISGSAADTQAVADAITYQL---GFHSIKLNEPPLVHTAARSFKEMCY-YREDLVAGIIMAGWDSQE
          IHDHI........A...A........GFHSI.LNE.PLVHTAA...KEMCY.Y...L.AGII.AGW..QE
Retrocopy IHDHIFCCCLGSAADTQAVADAVT*LGFHSIALNELPLVHTAASLLKEMCYQY*VNLMAGIIVAGWNPQE

Parental  GRQVYSVPIGGMMVRQPCAIGGSGSSYIYGYV
          G.Q.YS.P.G.MMVRQ..AI.GSGSSYIYG.V
Retrocopy GGQMYSAPMGDMMVRQSFAIRGSGSSYIYGCV

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_1807 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013390	2 retrocopies	retro_btau_1734, retro_btau_534,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Otolemur garnettii	ENSOGAG00000009653	1 retrocopy	retro_ogar_2114,
Pteropus vampyrus	ENSPVAG00000006048	1 retrocopy	retro_pvam_618,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tarsius syrichta	ENSTSYG00000010674	1 retrocopy	retro_tsyr_1807 ,