RetrogeneDB ID: retro_tsyr_1381

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_420742:51..550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDV3
• Ensembl ID: ENSTSYG00000011401
• Aliases: None
• Description: CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]

Sequence

>retro_tsyr_1381
CAGCAAAGATAGGTGGATTACAGCGGCTCAGAGATCAGGCAATGCAAATCAGTGAAAGGGAAGATGATCATGAGAAGAGA
GAAGATCAGGCGATAACTGGGAAGAAGGTGGAGGAGGTGCTGGTGGTGTAGAAAAGTCTTCAGGTCCCTGGAATAAAACA
GCTCCGGCCCAAACACCTCCTGCTCCTGTAATTGTTACAGAAACTCCAGAACCGGCAATGACTAGTGGTATGTATAGGCC
TCCTGGGGCCAGATTAACCACAACGAGAAAAACACCACAAGGACCACCAGAAATAGACAGCGACACACAGTTCCCATCCC
TGCAGTCAACTGCCAAGCACCTAGGAAGTTGGAAGGATAAAGAAATGGAGAAGAGCCTTGAAATAGTAAGACACAGAAAT
AGAGGCAGGGATGAGGTTTCCAAAAACCAGGCCCTTAAACTCCAACTAGACAACCAGCATGCTGTGCTTGAGAATCAGAA
AAGCAGCCACTCACAGTAC

Alignment

ORF - retro_tsyr_1381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.38 %
• Parental protein coverage: 94.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EQKEVDYSG-LRVQAMQISSEKEEDDNEKREDP-GDNWEEGGGGGGGVEKSSGPWNKAAPAQAPPAPVIV
          .Q..VDYSG.LR.QAMQIS....EDD.EKRED..GDNWEEGGGG.GGVEKSSGPWNK.APAQ.PPAPVIV
Retrocopy QQR*VDYSG<LRDQAMQIS--EREDDHEKREDQ<GDNWEEGGGGAGGVEKSSGPWNKTAPAQTPPAPVIV

Parental  TETPEPGMTSGVYRPPGARLTTTRKTPQGPPEIYSDTQFPSLQSTAKHLESRKDKEMEKSFEVVRHKNRG
          TETPEP.MTSG.YRPPGARLTTTRKTPQGPPEI.SDTQFPSLQSTAKHL.S.KDKEMEKS.E.VRH.NRG
Retrocopy TETPEPAMTSGMYRPPGARLTTTRKTPQGPPEIDSDTQFPSLQSTAKHLGSWKDKEMEKSLEIVRHRNRG

Parental  RDEVSKNQALKLQLANQYAVLENQKSSHSQY
          RDEVSKNQALKLQL.NQ.AVLENQKSSHSQY
Retrocopy RDEVSKNQALKLQLDNQHAVLENQKSSHSQY

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_1381 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460, retro_dnov_496, retro_dnov_656,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,
Tarsius syrichta	ENSTSYG00000011401	2 retrocopies	retro_tsyr_1381 , retro_tsyr_1759,