RetrogeneDB ID: retro_ogar_3360

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873801.1:412485..412984(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOC
• Ensembl ID: ENSOGAG00000027678
• Aliases: None
• Description: ras homolog family member C [Source:HGNC Symbol;Acc:669]

Sequence

>retro_ogar_3360
TTGTTGGTCTTCAGCAAGGCCCAATTCTGCAGAGATTTATGCACTCACAGTGTTTGAGAACTACCTGGCAGATATTGAGG
TGGATGGCAGGCAGGTAGAATTGGATTTGTGGAACACAGCTGGGCAGGAAGATCATGACTGCCTGAGGCCCCTCTCCTAC
CCAGACACCAATGTTTTACTGATGTGTTTCTCCATCAACAGCCCTAATAGTTTAGAAAACATCCCAGAAAAATGGACCCC
AGAAGTTGAGCATTTCTGCCCCAATGTGCCCATCATCCCGGTTGGGAAGAAGAAGGATCTTTGGAATAATGAGCATACAA
GGCGGGAGCTAGCCAAGATGGAATAGGAGCCCATAAAACCTGAAGAAGGCAGAGATATGGCAAACAGGATTGGTGCTTTG
GGGTACATGGAGTGTTCAGCAAAGACCAAAAATAGAGTGAGGGAGCTTTATGAAATGGCTATGAGAGCTGCTGTGCAAGC
CAGATGTGGGAAGAAAAAA

Alignment

ORF - retro_ogar_3360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.25 %
• Parental protein coverage: 86.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LIVFSKDQF-PEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPD
          L.VFSK.QF..E.Y..TVFENY.ADIEVDG.QVEL.LW.TAGQED.D.LRPLSYPDT.V.LMCFSI.SP.
Retrocopy LLVFSKAQF>AEIYALTVFENYLADIEVDGRQVELDLWNTAGQEDHDCLRPLSYPDTNVLLMCFSINSPN

Parental  SLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDMANRISAFGYLECS
          SLENIPEKWTPEV.HFCPNVPII.VG.KKDL...EHTRRELAKM..EP...EEGRDMANRI.A.GY.ECS
Retrocopy SLENIPEKWTPEVEHFCPNVPIIPVGKKKDLWNNEHTRRELAKME*EPIKPEEGRDMANRIGALGYMECS

Parental  AKTKEGVREVFEMATRAGLQVRKNKRR
          AKTK..VRE..EMA.RA..Q.R..K..
Retrocopy AKTKNRVRELYEMAMRAAVQARCGKKK

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_3360 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014299	1 retrocopy	retro_btau_1171,
Canis familiaris	ENSCAFG00000013413	1 retrocopy	retro_cfam_1152,
Callithrix jacchus	ENSCJAG00000013657	2 retrocopies	retro_cjac_1657, retro_cjac_2027,
Equus caballus	ENSECAG00000010174	3 retrocopies	retro_ecab_112, retro_ecab_257, retro_ecab_932,
Ficedula albicollis	ENSFALG00000000736	1 retrocopy	retro_falb_11,
Gorilla gorilla	ENSGGOG00000002741	2 retrocopies	retro_ggor_18, retro_ggor_732,
Macropus eugenii	ENSMEUG00000004807	1 retrocopy	retro_meug_37,
Monodelphis domestica	ENSMODG00000000981	1 retrocopy	retro_mdom_1245,
Otolemur garnettii	ENSOGAG00000027678	3 retrocopies	retro_ogar_2606, retro_ogar_3360 , retro_ogar_58,
Otolemur garnettii	ENSOGAG00000028489	1 retrocopy	retro_ogar_2340,
Sarcophilus harrisii	ENSSHAG00000001981	1 retrocopy	retro_shar_455,
Taeniopygia guttata	ENSTGUG00000017533	1 retrocopy	retro_tgut_11,
Tetraodon nigroviridis	ENSTNIG00000015041	1 retrocopy	retro_tnig_2,
Xenopus tropicalis	ENSXETG00000006898	1 retrocopy	retro_xtro_15,
Xiphophorus maculatus	ENSXMAG00000008103	1 retrocopy	retro_xmac_13,