RetrogeneDB ID: retro_ogar_3270

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873762.1:485070..485876(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1A2
• Ensembl ID: ENSOGAG00000004630
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 2 [Source:HGNC Symbol;Acc:3192]

Sequence

>retro_ogar_3270
AAGACTCATATCAACATCATCGTCATTGGACACACAGATTTGGGCGAGTCCACCACTACTGGCCATCTGATCTACAAATG
TGGTGGTATTGACAAGAGAACCATTGAAAAATTTGAGAAGGAGGCTGTTTAGATGGGAAAGGGCTCCTTCAAGTATGCCT
GGGTCTTGGATAAACTGAAGGTTGAGCATGAATGTAGTATCACCATTGATATCTCCCTGTGGAAATTTGAGACCAGCAGA
TACTACGTGACTATCATTGATGCCCCAAGACACAGAGACTTCATCAAAAACATGATTACAGGCACATCTCAGGCTGACTG
TGCTGGCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCAAAGAATGGGCAGACCTGTGAGCATGCCC
TTCGGGCTTACACACTGGGTGTGAAGCAACTAATTGTTGGTGTGAACAAGATGGATTCCACTGAGCCACCCTACAGCCAG
AAGAGATATGAGGAAATCATTAAGGAAGTCAGCACTTACATTAAGAAAATTGGCTACAACCTTGACAGAGTAGCATTTGT
GCCAATTTCTGGTTGGAATGGTGACAACACGTTGGAGCCAAGTGCAAACATGCCTTGGTTCAAAGGATGGAAAGTCACCT
GGAAGGATGTCAATGCCAGTGGAACCACGTTGCTTGAAGCTCTGGATTCATTCTGCCACCAACGCGTCCAACTGACAAGC
CCTTGCATCTGCTTCTGCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTCCCTGTGGGCCAAGTTGAGACTGGTGTT
CTCAAA

Alignment

ORF - retro_ogar_3270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 58.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITID
          KTHINI.VIGH.D.G.STTTGHLIYKCGGIDKRTIEKFEKEA..MGKGSFKYAWVLDKLK.E.E..ITID
Retrocopy KTHINIIVIGHTDLGESTTTGHLIYKCGGIDKRTIEKFEKEAV*MGKGSFKYAWVLDKLKVEHECSITID

Parental  ISLWKFETTKYYITIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLG
          ISLWKFET..YY.TIIDAP.HRDFIKNMITGTSQADCA.LIVAAGVGEFEAGISKNGQT.EHAL.AYTLG
Retrocopy ISLWKFETSRYYVTIIDAPRHRDFIKNMITGTSQADCAGLIVAAGVGEFEAGISKNGQTCEHALRAYTLG

Parental  VKQLIVGVNKMDSTEPAYSEKRYDEIVKEVSAYIKKIGYNPATVPFVPISGWHGDNMLEPSPNMPWFKGW
          VKQLIVGVNKMDSTEP.YS.KRY.EI.KEVS.YIKKIGYN...V.FVPISGW.GDN.LEPS.NMPWFKGW
Retrocopy VKQLIVGVNKMDSTEPPYSQKRYEEIIKEVSTYIKKIGYNLDRVAFVPISGWNGDNTLEPSANMPWFKGW

Parental  KVERKEGNASGVSLLEALDT-ILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGILR
          KV..K..NASG..LLEALD..ILPPTRPTDKPL.L.LQDVYKIGGIGTVPVG.VETG.L.
Retrocopy KVTWKDVNASGTTLLEALDS<ILPPTRPTDKPLHLLLQDVYKIGGIGTVPVGQVETGVLK

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_3270 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 14 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Latimeria chalumnae	ENSLACG00000002952	1 retrocopy	retro_lcha_39,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macropus eugenii	ENSMEUG00000005018	23 retrocopies	retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Myotis lucifugus	ENSMLUG00000016760	1 retrocopy	retro_mluc_1250,
Mustela putorius furo	ENSMPUG00000008289	3 retrocopies	retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11, retro_nleu_1489,
Ornithorhynchus anatinus	ENSOANG00000004908	1 retrocopy	retro_oana_73,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270 , retro_ogar_643,
Otolemur garnettii	ENSOGAG00000009152	10 retrocopies	retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Ictidomys tridecemlineatus	ENSSTOG00000028862	1 retrocopy	retro_itri_1028,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,