RetrogeneDB ID: retro_ogar_1225

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873539.1:6876695..6877284(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSOGAG00000013749
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:HGNC Symbol;Acc:30246]

Sequence

>retro_ogar_1225
CTGGTCCATCAAACTCATATGTCATCCTGTTGGGTGGATAGGCCCTCCGAGATAGTAGATGTTGGAGACAAAGTATGGGT
GAAGCTTATTGGCCAAGAGATGAACAACGATAGGATAAATGTATCCCTCTCCATGAAAGTTGTCAACCAAAGGCCTGGGA
AAGACCTTGATCCCAACAATGTTATCATTGAGCAAGAAGAGAGAAGGAGATGTTCCTGCCAGGATTACACTGGGCAGAAG
ATCACTCTGGAGGCTGTCCTGAGCACTACCTGCGAGAAGTGTGGTTGTCAAGGCCCCTGTGCAAAAGACTGCTTCATGCA
ACCGGTGGGACCAAATACTCTCTGATACTTGATGAGGAAGAAGAGAAGGAAGAGGCAAAGTCAGCAGAGTTTGAGAAGCC
TGACCCCATGAAGAATTCTAAAAAAAGAAAGAAGGAAAGAAGATCAAGAAACATAGAGACAGGAAGCCATCTGACTCTGA
CAGCTCAGACTCTGAGAGTTATACAGGCAAGAGGTGAAGGCACACATCAAAAGACAGCAAGGCAGCAAAGAAGACGAAAA
AGAAGCAGCATAAGAACAAGCACAAGGAG

Alignment

ORF - retro_ogar_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 82.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIEQEERRR
          LVH.THMSSC.VD.PSEIVDVGDKVWVKLIG.EM.NDRI.VSLSMKVVNQ..GKDLDPNNVIIEQEERRR
Retrocopy LVHQTHMSSCWVDRPSEIVDVGDKVWVKLIGQEMNNDRINVSLSMKVVNQRPGKDLDPNNVIIEQEERRR

Parental  RSFQDYTGQKITLEAVLNTTCKKCGCKGHFAKDCFTQP-GGTKYSLIPDEEEEEEEAKSAEFEKPDPMKN
          .S.QDYTGQKITLEAVL.TTC.KCGC.G..AKDCF.QP.GGTKYSLI.DEEEE.EEAKSAEFEKPDPMKN
Retrocopy CSCQDYTGQKITLEAVLSTTCEKCGCQGPCAKDCFMQP<GGTKYSLILDEEEEKEEAKSAEFEKPDPMKN

Parental  SSRKRKKE-KKKKKHRDRKSSDSDSSDSESDIGKRSRHTSKDSKAAKKKKKKKKHKKKHKD
          .S.KRKKE.KK.KKHRDRK.SDSDSSDSES..GKR.RHTSKDSKAA.KK.KKK.HK.KHK.
Retrocopy -SKKRKKE<KKIKKHRDRKPSDSDSSDSESYTGKR*RHTSKDSKAA-KKTKKKQHKNKHKE

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_1225 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225 ,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,