RetrogeneDB ID: retro_tsyr_71

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_1635:27469..27817(+)
• Located in intron of: ENSTSYG00000002041

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD302
• Ensembl ID: ENSTSYG00000002564
• Aliases: None
• Description: CD302 molecule [Source:HGNC Symbol;Acc:30843]

Sequence

>retro_tsyr_71
TGTCCTTCATTCACCTGGGTGCAGTTTCAAGGCAGCTATTACATTTTTCTTCAAGAAGCCATCAAAGTAGAAAGCATAGA
GGATGTCAGAAATCAGTGTACTGACCATGGAGCAGACATGATAAGCATACATAATGAGGAAGAAAATGCTTTTGTACTGA
ATAATTTTAAAAAGCAGTGGAAAGGCCCAGATAATATCCTACTAGGCATGTTTTATGACACAGATGATGAAAGTTTCAAG
TGGGTTGATAATTCAAATATGACATTTGATAAGCGGACAGACCATGAAGATGGTGAGGATCTAGTTGACAACTGTGCTTT
TTTGCACACCAAGACAGGTGAATGGAAA

Alignment

ORF - retro_tsyr_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.17 %
• Parental protein coverage: 56.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CPSSTWVQFQDSCYIXLQCGGIQAFKVESIEDVRNQCTDHGADMISIHNEEENAFILDTLKKQWKGPDDI
          CPS.TWVQFQ.S.YI.LQ.....A.KVESIEDVRNQCTDHGADMISIHNEEENAF.L...KKQWKGPD.I
Retrocopy CPSFTWVQFQGSYYIFLQ----EAIKVESIEDVRNQCTDHGADMISIHNEEENAFVLNNFKKQWKGPDNI

Parental  LLGMFYDTDDESFKWFDNSNMTFDKWTDQEDGEDLVDTCAFLHTKTGEWK
          LLGMFYDTDDESFKW.DNSNMTFDK.TD.EDGEDLVD.CAFLHTKTGEWK
Retrocopy LLGMFYDTDDESFKWVDNSNMTFDKRTDHEDGEDLVDNCAFLHTKTGEWK

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_71 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007947	2 retrocopies	retro_chof_224, retro_chof_2460,
Oryctolagus cuniculus	ENSOCUG00000016361	1 retrocopy	retro_ocun_927,
Tarsius syrichta	ENSTSYG00000002564	1 retrocopy	retro_tsyr_71 ,