RetrogeneDB ID: retro_ogar_1306

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873542.1:16575844..16576117(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000025809
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRTCAP2
• Ensembl ID: ENSOGAG00000030271
• Aliases: None
• Description: keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:28942]

Sequence

>retro_ogar_1306
TACTCGGCTCCGTTCTCGGCTAGTGGGGCCATCGGGACACACGGGCCGGACATGACAGTGGTGGGGACAGGCGCGTCCCT
GGCACTCCCCGCTCTGCCGCCCCTGCTGCTCTTGGCAGAACGTAGATGTACAGCCGCCAGCTGCCTCCACCAAGTGGCTC
CCTATCTGGGGCACCTGCGTGGCTCCGGCCTCTTCATCTTTTCTCTCACTGCCTTCAAGAATCTGGAGACCCTTGTCTTT
GGCAAAGGATTCCAAGCAAAAATTTTCCTTGAG

Alignment

ORF - retro_ogar_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.37 %
• Parental protein coverage: 92. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FGSRFSASGADWTHGRGVMVVGTGTSLALSSLLSLLLFAGMQ-MYSRQL-ASTEWLTIQGG-LLGSGLFV
          ....FSASGA..THG....VVGTG.SLAL..L..LLL.A....MYSRQL.AST.WL.I.G..L.GSGLF.
Retrocopy YSAPFSASGAIGTHGPDMTVVGTGASLALPALPPLLLLAERR<MYSRQL<ASTKWLPIWGT<LRGSGLFI

Parental  FSLTAFNNLENLVFGKGFQAKIFPE
          FSLTAF.NLE.LVFGKGFQAKIF.E
Retrocopy FSLTAFKNLETLVFGKGFQAKIFLE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1306 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306 ,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,