RetrogeneDB ID: retro_tsyr_21

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_527813:3..771(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000005072
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PSMA4
• Ensembl ID: ENSTSYG00000011745
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 4 [Source:HGNC Symbol;Acc:9533]

Sequence

>retro_tsyr_21
TCTCGAAGATATGACTCCAGGACCACTATATTTTCCCCAGAAGGTCGCCTATACCAAGTTGAATATGCCATGGAAGCTAT
TGGACATGCAGGCACCTGTTTGGGAATTTTAGCAAACGATGGGGTTTTGCTTGCAGCAGAGAGACGTAACATCCACAAGC
TCCTCGATGAAGTCTTTTTTTCCGAAAAAATTTATAAACTCAATGAGGACATGGCCTGCAGTGTGGCAGGCATAACTTCG
GATGCTAACGTTCTGACTAATGAACTGAGGCTCATTGCTCAAAGGTATTTATTACAGTATCAGGAGCCAATTCCTTGTGA
GCAGTTGGTTACAGCATTGTGTGATATCAAGCAAGCTTATACACAGTTTGGAGGTAAACGTCCCTTTGGTGTTTCATTGC
TGTATATTGGCTGGGATAAGCACTATGGCTTTCAGCTCTACCAGAGTGACCCTAGTGGAAATTATGGGGGATGGAAAGCC
ACATGCATTGGAAATAATAGTGCTGCAGCTGTGTCAATGTTGAAACAAGACTACAAAGAAGGAGAGATGACTTTGAAGTC
AGCACTTGCTTTAGCTATTAAGGTGCTAAATAAGACCATGGATGTTAGTAAACTGTCTGCTGAAAAAGTGGAAATTGCGA
CTCTGACAAGGGAGAATGGAAAGACGGTAATCAGAGTTCTCAAACAAAAAGAAGTGGAACAGTTGATCAAAAAGCATGAG
GAAGAAGAAGCTAAGGCTGAGCGTGAGAAGAAGGAGAAAGAACAGAAA

Alignment

ORF - retro_tsyr_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.46 %
• Parental protein coverage: 97.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKNY-LNGDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGV
          EK.Y.LN.DMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGV
Retrocopy EKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQAYTQFGGKRPFGV

Parental  SLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMD
          SLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMD
Retrocopy SLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTMD

Parental  VSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQK
          VSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQK
Retrocopy VSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKHEEEEAKAEREKKEKEQK

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_21 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035, retro_mmus_1707,
Pteropus vampyrus	ENSPVAG00000009182	2 retrocopies	retro_pvam_1229, retro_pvam_824,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324, retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21 ,