RetrogeneDB ID: retro_tsyr_1640

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_525420:101..869(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000011133
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKACB
• Ensembl ID: ENSTSYG00000000380
• Aliases: None
• Description: protein kinase, cAMP-dependent, catalytic, beta [Source:HGNC Symbol;Acc:9381]

Sequence

>retro_tsyr_1640
AGCGGGAAAGAGTTTCTAGCCAAAGCCAAAGAAGACTTTTTGAAAAATGGGAGAATCCTGCTCCAAATAATGCTGGACTT
GAGGATTTTGAAAAGAAAAAGACCCTTGGAACAGGCTCATTTGGAAGAGTAATGTTGGTGAAGCATAAGGCCACTGAACA
GTATTATGCCATGAAGATTTTAGATAAGCAGAAGGTTGTTAAACTGAAGCAAATAGAGCATACTTTGAATGAGAAAAGAA
TATTACAGGCAGTGAATTTTCCTTTTCTTGTTCAACTGGAATATTCTTTTAAGGATAATTCTAATTTATACATGGCTATA
GAATATGTCCCTGGGGGTGAAATGTTTTCACATCTAAGAAGAATTGGAAGGCTCAGTGAACCCCATGCATGGTTCTATGC
AGCTCAGATAGTGCTAACATTTGAGTACCTCCACTCTCTAGACCTCATCTACAGAGATCTGAAACCTGAAAATCTCTTAA
TCGACCATCGAGGTTAGATCCAGGTCACAGACTTTGGGTTTGCCAAAAGAGTTAAAGGAACTTGGACATTATGTGGCACT
CCAGAGTATCTGGATCTGGAAATAATCCTCAGCAAGGGCTACAATAAAGCAGTGGATTGGTGGGCTTTAGTAGTGCTAAT
CTATGAAAGGGCAGCTGGCTAACCCCCATTCTTTGCAGACCAGCCAATTCAGATTTATGAAAAAGATTGTTTTTGGAAAG
GTCTGATTCCCATCCCACTTCAGTTCAGATCTCAAGGACCTTCTACAG

Alignment

ORF - retro_tsyr_1640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 64.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMKEFLAKAKEDFLK-KWENPAPNNAGLEDFERKKTLGTGSFGRVMLVKHKATEQYYAMKILDKQKVVKL
          S.KEFLAKAKEDFLK.KWENPAPNNAGLEDFE.KKTLGTGSFGRVMLVKHKATEQYYAMKILDKQKVVKL
Retrocopy SGKEFLAKAKEDFLK<KWENPAPNNAGLEDFEKKKTLGTGSFGRVMLVKHKATEQYYAMKILDKQKVVKL

Parental  KQIEHTLNEKRILQAVNFPFLVRLEYSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVL
          KQIEHTLNEKRILQAVNFPFLV.LEYSFKDNSNLYM..EYVPGGEMFSHLRRIGR.SEPHA.FYAAQIVL
Retrocopy KQIEHTLNEKRILQAVNFPFLVQLEYSFKDNSNLYMAIEYVPGGEMFSHLRRIGRLSEPHAWFYAAQIVL

Parental  TFEYLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWW
          TFEYLHSLDLIYRDLKPENLLIDH.G.IQVTDFGFAKRVKG.TWTLCGTPEYL..EIILSKGYNKAVDWW
Retrocopy TFEYLHSLDLIYRDLKPENLLIDHRG*IQVTDFGFAKRVKG-TWTLCGTPEYLDLEIILSKGYNKAVDWW

Parental  ALGVLIYEMAAGYPPFFADQPIQIYE-KIVSGKVRFPSHFSSDLKDLLR
          AL.VLIYE.AAG.PPFFADQPIQIYE.KIV.GKV.FPSHFSSDLKDLL.
Retrocopy ALVVLIYERAAG*PPFFADQPIQIYE>KIVFGKV*FPSHFSSDLKDLLQ

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_1640 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003457	1 retrocopy	retro_mmul_186,
Nomascus leucogenys	ENSNLEG00000009888	1 retrocopy	retro_nleu_2469,
Pongo abelii	ENSPPYG00000001209	1 retrocopy	retro_pabe_61,
Rattus norvegicus	ENSRNOG00000004978	1 retrocopy	retro_rnor_519,
Tarsius syrichta	ENSTSYG00000000380	2 retrocopies	retro_tsyr_1640 , retro_tsyr_1802,