RetrogeneDB ID: retro_tsyr_1135

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_31819:10372..11061(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000006737
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP2R5A
• Ensembl ID: ENSTSYG00000013786
• Aliases: None
• Description: protein phosphatase 2, regulatory subunit B', alpha [Source:HGNC Symbol;Acc:9309]

Sequence

>retro_tsyr_1135
TTATATGAAACAGAACATTTCAATGGTATTGCTGAACTCCTCAAAATATTAGGAAATATTACCAACGGGCTTTGCATTGC
CACTGAAAGCAGAACATAATTTCTAATGAAGCTTCTTATTCCTATGCATACTGTAAAAGGATTAGCTTTGTTTCATGTTC
AGCTAGCATATTGTGTCGTACAGTTCCTGGAGAAAGATACAACACTAACAGAACCAGTGATCAGAGGTCTGCTGAAATTT
TGGCCAAAAACGTGCAGTCAGAAAGAGGTGATGTTTTTAGGAGAAATTGAAGAAATCTTAGATATCGTTGAACCAACACA
GTTCAAAAAAATTGAAGAGCCACTTTTTAAGCAGATATCCAAGTGTGTATCCAATTCTCATTTCCAGGTTGTAGAAAGGG
CATTGTACTTCTGGAATACTGAATATATCCTTAGTTTAACTGAGGAGAATATTGATAAATTTCTGCCAATTATGTTTGCC
AGTTTGTACAAATTTCCAAAGAACACTGGAATCTGACCATTGTAACCCTAGTACACAATGTGCTGAAAACCCTAATGGGA
ATGAATGGCAAGCTTTTTGAGGACCTTACTAGCTCATACAAAGCTGAAAGACAGAGTGAGGAAAAGAAGGAATTGGAATG
TGAAAAATTATGGAAACAATTAGAGGAGCTAAAGCTAAAGAAAGCTCTA

Alignment

ORF - retro_tsyr_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 54.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IYETEHFNGVAELLEILGSIINGFALPLKAEHKQFLMKVLIPMHTAKGLALFHAQXXXXXXXXXXXXXXX
          .YETEHFNG.AELL.ILG.I.NG...........FLMK.LIPMHT.KGLALFH.Q...............
Retrocopy LYETEHFNGIAELLKILGNITNGLCIATESR-T*FLMKLLIPMHTVKGLALFHVQLAYCVVQFLEKDTTL

Parental  XXXVIRGLLKFWPKTCSQKEVMFLGEIEEILDVIEPTQFKKIEEPLFKQISKCVSSSHFQVAERALYFWN
          ...VIRGLLKFWPKTCSQKEVMFLGEIEEILD..EPTQFKKIEEPLFKQISKCVS.SHFQV.ERALYFWN
Retrocopy TEPVIRGLLKFWPKTCSQKEVMFLGEIEEILDIVEPTQFKKIEEPLFKQISKCVSNSHFQVVERALYFWN

Parental  NEYILSLIEENIDKILPIMFASLYK-ISKEHWNPTIVTLVYNVLKTLMEMNGKLFEDLTSSYKAERQREK
          .EYILSL.EENIDK.LPIMFASLYK.ISKEHWN.TIVTLV.NVLKTLM.MNGKLFEDLTSSYKAERQ.E.
Retrocopy TEYILSLTEENIDKFLPIMFASLYK<ISKEHWNLTIVTLVHNVLKTLMGMNGKLFEDLTSSYKAERQSEE

Parental  KKELEREELWKKLEELKLKKAL
          KKELE.E.LWK.LEELKLKKAL
Retrocopy KKELECEKLWKQLEELKLKKAL

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_1135 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009549	1 retrocopy	retro_mluc_1768,
Mus musculus	ENSMUSG00000026626	5 retrocopies	retro_mmus_2410, retro_mmus_2415, retro_mmus_2417, retro_mmus_2421, retro_mmus_3390,
Pteropus vampyrus	ENSPVAG00000010468	1 retrocopy	retro_pvam_1209,
Rattus norvegicus	ENSRNOG00000000068	1 retrocopy	retro_rnor_2107,
Tarsius syrichta	ENSTSYG00000013786	1 retrocopy	retro_tsyr_1135 ,
Vicugna pacos	ENSVPAG00000011662	1 retrocopy	retro_vpac_63,