RetrogeneDB ID: retro_tsyr_2111

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_92133:8331..8876(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000004044
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM49A
• Ensembl ID: ENSTSYG00000010693
• Aliases: None
• Description: family with sequence similarity 49, member A [Source:HGNC Symbol;Acc:25373]

Sequence

>retro_tsyr_2111
TTTGACGAACTCAAGATGACAGATCCTGCCATACAGAATGATTTCAGCTATTTAGAAGAACATTGAGTCGTAAGAGGATT
AATAATGTACCAGTAGAAGGAGAATATGAAGTAAATAACGAGTTGGCGATCCGAATGTCTTTGTTTTATGCTGAGGCGAC
TCCAATGCTGAAAACCTTGAGTGATGCCACCACGAAATTTGTATCCGAGAATAAAAATTTACCGATAGAAAATACGACCG
ACGGTTTAAGCACCATGGCTAGTGTATGCAGAGTCATAATGGAAACACCGGAATGCAGAAACAGGTTTGCAAACGAGACA
GTGTCGTTCTGCTTGAGGGTGATGGTGGGCATCATGATACTCTATGATCACATGCATCCAGTGGGAGCATTTGCCAAAAC
TTCCAAAATCAATATGAAAGGTTGTATCAAAGTTCTTAAGGACCAGCCTCCCAACAGTGTAGAAGGTCTTCTAAATGCTC
TCAGGTACACAGCAAAACATTTGAATGATGAGACTACCTCCAAGCAAATTAAATCCATGCTGCAA

Alignment

ORF - retro_tsyr_2111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 56.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FDELKMRNPAIQNDFSY-YRRTISRNRINNMHLDIENEVNNEMANRMSLFYAEATPMLKTLSNATMHFVS
          FDELKM..PAIQNDFSY..RRT.SR.RINN.....E.EVNNE.A.RMSLFYAEATPMLKTLS.AT..FVS
Retrocopy FDELKMTDPAIQNDFSY<FRRTLSRKRINNVPVEGEYEVNNELAIRMSLFYAEATPMLKTLSDATTKFVS

Parental  ENKTLPIENTTDCLSTMTSVCKVMLETPEYRSRFSEETL-MCMRVMVGVIILYDHVHPVGAFCKTSKIDM
          ENK.LPIENTTD.LSTM.SVC.V..ETPE.R.RF..ET...C.RVMVG..ILYDH.HPVGAF.KTSKI.M
Retrocopy ENKNLPIENTTDGLSTMASVCRVIMETPECRNRFANETVSFCLRVMVGIMILYDHMHPVGAFAKTSKINM

Parental  KGCIKVLKEQAPDSVEGLLNALRFTTKHLNDESTSKQIRAMLQ
          KGCIKVLK.Q.P.SVEGLLNALR.T.KHLNDE.TSKQI..MLQ
Retrocopy KGCIKVLKDQPPNSVEGLLNALRYTAKHLNDETTSKQIKSMLQ

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_2111 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012839	1 retrocopy	retro_cpor_68,
Microcebus murinus	ENSMICG00000013924	1 retrocopy	retro_mmur_898,
Tarsius syrichta	ENSTSYG00000010693	4 retrocopies	retro_tsyr_1129, retro_tsyr_1823, retro_tsyr_2111 , retro_tsyr_827,