RetrogeneDB ID: retro_tsyr_317

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_7939:28668..28950(+)
• Located in intron of: ENSTSYG00000003189

Retrocopy information

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

Parental gene information

• Parental gene symbol: EFCAB2
• Ensembl ID: ENSTSYG00000006254
• Aliases: None
• Description: EF-hand calcium binding domain 2 [Source:HGNC Symbol;Acc:28166]

Sequence

>retro_tsyr_317
GAGTTAGCTGCAGCAGAATTTCACAAAAAAATCAAAGAGGCATCTGAAGTGTTTGACCATGAGTCAAATAATACAGTGGA
TGTAAGAGAGATTGGAACAGTTATCAGCTCATTAGGATGCTGTCCTAATGAAGGAGAGCTACATGATCTAATTGCAGAGG
TAAAGGAAGAAGAACCCACTGGATGCATCTGATTTGAAAAATTTCTTCCAGTGACGACCCAAGTACTACTAGAAAGAAAA
TACAGCCCAATGCCAGAAGATGTTCTCCTTTGAACTTTTAAA

Alignment

ORF - retro_tsyr_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.11 %
• Parental protein coverage: 61.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELAAAEFHKKIKEAFEVFDHESNNTVDVREIGTIIRSLGCCPSEGELHDLIAEVEEEEPTGYIRFEKFLP
          ELAAAEFHKKIKEA.EVFDHESNNTVDVREIGT.I.SLGCCP.EGELHDLIAEV.EEEPTG.I.FEKFLP
Retrocopy ELAAAEFHKKIKEASEVFDHESNNTVDVREIGTVISSLGCCPNEGELHDLIAEVKEEEPTGCI*FEKFLP

Parental  VMTQVLLER-YRPIPEDVLLRAFE
          V.TQVLLER.Y.P.PEDVLL..F.
Retrocopy VTTQVLLERKYSPMPEDVLL*TFK

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_317 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029154	1 retrocopy	retro_cfam_781,
Callithrix jacchus	ENSCJAG00000016907	1 retrocopy	retro_cjac_3944,
Equus caballus	ENSECAG00000022403	1 retrocopy	retro_ecab_874,
Oryctolagus cuniculus	ENSOCUG00000029593	1 retrocopy	retro_ocun_612,
Tarsius syrichta	ENSTSYG00000003831	2 retrocopies	retro_tsyr_1142, retro_tsyr_36,
Tarsius syrichta	ENSTSYG00000006254	2 retrocopies	retro_tsyr_1584, retro_tsyr_317 ,