RetrogeneDB ID: retro_tsyr_1215

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_35023:6315..6691(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSTSYG00000013060
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_tsyr_1215
CGTGAAAATTTCAGTAATCTCACCTCATGGTTAGAGGATACCTGGCAGCATTGCAGTTGCAGCATGGTTATCATGCTAAT
TGGAAATAAAAGTGACCTAGTGTCCCATAGAGATGTGATAAGAGAAGAAGGGAAGGCCTTTCCTTGGGAGCATGGACTTA
TATTCATGAAATCTTTAGTAGCCAAAACGACCTGTGATATACGAGGGGTCTTCATGAACACAACCAATGAAATATTTAGA
AGATTCAGTAGGGTCTCTTTAATGTCCACAGCTAAGCAAATGGCATCAAGATTGGGCCCCAACAGTCAATGTTAATGTCA
GTGGAATGGCATCACAGTGGAACTCTTGTGACAAAGGATCCAACTCTGGCTGCTGC

Alignment

ORF - retro_tsyr_1215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.78 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESRREVKKEEGEAFAREHGLIFMET-SAKTASNVEEA
          R..F..LT.WLED..QH....MVIMLIGNKSDL.S.R.V..EEG.AF..EHGLIFM....AKT.......
Retrocopy RENFSNLTSWLEDTWQHCSCSMVIMLIGNKSDLVSHRDVIREEGKAFPWEHGLIFMKSLVAKTTCDIRGV

Parental  FINTAKEIYE-KIQEGVFDINNEANGIKIGPQHAATNAT---HAG-NQGGQQAGGGCC
          F.NT..EI...KIQ.G.F.....ANGIKIGPQ..........H.G.N........GCC
Retrocopy FMNTTNEIFR<KIQ*GLFNVHS*ANGIKIGPQQSMLMSVEWHHSG<NSCDKGSNSGCC

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_1215 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007153	1 retrocopy	retro_cfam_2057,
Equus caballus	ENSECAG00000012124	1 retrocopy	retro_ecab_970,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Sorex araneus	ENSSARG00000013511	2 retrocopies	retro_sara_688, retro_sara_744,
Tarsius syrichta	ENSTSYG00000013060	1 retrocopy	retro_tsyr_1215 ,
Tarsius syrichta	ENSTSYG00000014758	1 retrocopy	retro_tsyr_802,
Tursiops truncatus	ENSTTRG00000009615	1 retrocopy	retro_ttru_1377,