RetrogeneDB ID: retro_amel_1304

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193175.1:310331..310699(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSAMEG00000016456
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_amel_1304
ACCGGCTCGGGGTGCTGCGAGCAGAACATCAAACGGATGGGCACCTTTAGCTCTGTGGAACAGTCCGGAAGGTTTTACAG
CCTCCACGTGGTACCTCCCTGGAATATGACAGGCCATGGTGGCTTCCTTCCCTGCAAAGAGGGAATGAAGCCCATGTGGG
AAGATGATGCAAACAAAAAAGGTGGCAAGTGCGTTATCTGGCTGTGGAAGGGCTTGGCGTGCTGTTGCTGGGAGAATCTC
ATCCTGGTCGCATTGAGGCAGCAGTTCACGGTGGGGAGGAAATCTGCGGATCTGTGTGGTGTCAGGAGGATATCATTTCA
CTATAGAATAAGACTGGCAGAGACCTAGCAACCACAGCCCGAAGACGG

Alignment

ORF - retro_amel_1304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.57 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSSQSYEQNIKQIGTFASVEQFWRFYS-HMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRK
          T.S...EQNIK..GTF.SVEQ..RFYS.H.V.P...TGH..F...KEG.KPMWEDDANK.GGK..I.L.K
Retrocopy TGSGCCEQNIKRMGTFSSVEQSGRFYSLHVVPPWNMTGHGGFLPCKEGMKPMWEDDANKKGGKCVIWLWK

Parental  GLASRCWENLILAMLGEQFMV-GEEICGAVVSVRFQEDIISIWNKTASDQATTARIR
          GLA..CWENLIL..L..QF.V.GEEICG...SV..QEDIIS..NKT..D.ATTAR.R
Retrocopy GLACCCWENLILVALRQQFTV<GEEICG---SVWCQEDIISL*NKTGRDLATTARRR

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1304 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1304 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304 ,
Bos taurus	ENSBTAG00000010598	2 retrocopies	retro_btau_1232, retro_btau_1498,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Choloepus hoffmanni	ENSCHOG00000013109	3 retrocopies	retro_chof_1963, retro_chof_369, retro_chof_567,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57, retro_eeur_668,
Echinops telfairi	ENSETEG00000007930	1 retrocopy	retro_etel_1385,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Nomascus leucogenys	ENSNLEG00000014333	1 retrocopy	retro_nleu_1189,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
Ictidomys tridecemlineatus	ENSSTOG00000003508	3 retrocopies	retro_itri_1270, retro_itri_1370, retro_itri_573,