RetrogeneDB ID: retro_lafr_1185

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_84:1340164..1340550(-)
• Located in intron of: ENSLAFG00000017203

Retrocopy information

• Ensembl ID: ENSLAFG00000028372
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTSF1
• Ensembl ID: ENSLAFG00000016318
• Aliases: None
• Description: None

Sequence

>retro_lafr_1185
CAGAATCATCCTGATGTCACAAACAAGGTGGCTCCTTGTCCCTTCAGTGCTCACCACCAGGTTCCTCAGGTGAAATCAGC
CATCATATCTCAAGCCGTGATGACAAAAGTTGTATTGAGCAGCATGTTGTCGACCAAATGAGGAACCTTGGACAAGAGAC
TCTGGCTAAGAGCACATGGCAGTGCCCTTCTTGTGACAAAGACTGGGATAAAGATTTATGGGAACAGATCAGCACCCTAT
TTGTCTGGGGCACAGCCAACTACTGTGGCAACAACAGCCCTGCAAGCAACATAGTTATAGAACATAAGAGTAACCTGGCT
TCAGGCATGCGTGTTCGCAAGTCTCTGCTATATGTTCTGCCCTGGAAAAACAATGGAAATGCACAG

Alignment

ORF - retro_lafr_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 77.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNHPDVANKLATCPFNARHQVPRA-EISHHISSCDDKSCIEQDVVNQTRNLGQETLAESTWQCPPCDEDW
          .NHPDV.NK.A.CPF.A.HQVP...EISHHISS.DDKSCIEQ.VV.Q.RNLGQETLA.STWQCP.CD.DW
Retrocopy QNHPDVTNKVAPCPFSAHHQVPQV<EISHHISSRDDKSCIEQHVVDQMRNLGQETLAKSTWQCPSCDKDW

Parental  DKDLWEQTSTPFVWGTANYCGNNSPASNIVMEHKSNLASGMRVPKSLPYVLPWKNNGNAQ
          DKDLWEQ.ST.FVWGTANYCGNNSPASNIV.EHKSNLASGMRV.KSL.YVLPWKNNGNAQ
Retrocopy DKDLWEQISTLFVWGTANYCGNNSPASNIVIEHKSNLASGMRVRKSLLYVLPWKNNGNAQ

Legend:

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

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_1185 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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 20 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014260	3 retrocopies	retro_acar_135, retro_acar_143, retro_acar_92,
Ailuropoda melanoleuca	ENSAMEG00000000939	6 retrocopies	retro_amel_1420, retro_amel_324, retro_amel_338, retro_amel_639, retro_amel_724, retro_amel_796,
Bos taurus	ENSBTAG00000018085	1 retrocopy	retro_btau_1316,
Canis familiaris	ENSCAFG00000006465	2 retrocopies	retro_cfam_377, retro_cfam_592,
Choloepus hoffmanni	ENSCHOG00000001659	2 retrocopies	retro_chof_1261, retro_chof_950,
Callithrix jacchus	ENSCJAG00000018968	1 retrocopy	retro_cjac_904,
Dasypus novemcinctus	ENSDNOG00000001438	4 retrocopies	retro_dnov_2233, retro_dnov_2536, retro_dnov_256, retro_dnov_76,
Equus caballus	ENSECAG00000013618	2 retrocopies	retro_ecab_688, retro_ecab_806,
Echinops telfairi	ENSETEG00000009310	1 retrocopy	retro_etel_1619,
Felis catus	ENSFCAG00000010156	5 retrocopies	retro_fcat_1252, retro_fcat_1302, retro_fcat_1543, retro_fcat_557, retro_fcat_940,
Loxodonta africana	ENSLAFG00000016318	1 retrocopy	retro_lafr_1185 ,
Macropus eugenii	ENSMEUG00000016206	1 retrocopy	retro_meug_942,
Microcebus murinus	ENSMICG00000008444	1 retrocopy	retro_mmur_842,
Myotis lucifugus	ENSMLUG00000012961	3 retrocopies	retro_mluc_1177, retro_mluc_1286, retro_mluc_56,
Mustela putorius furo	ENSMPUG00000005669	3 retrocopies	retro_mputfur_1249, retro_mputfur_155, retro_mputfur_62,
Otolemur garnettii	ENSOGAG00000017227	2 retrocopies	retro_ogar_2617, retro_ogar_3251,
Rattus norvegicus	ENSRNOG00000036831	1 retrocopy	retro_rnor_2525,
Tarsius syrichta	ENSTSYG00000004679	2 retrocopies	retro_tsyr_1437, retro_tsyr_1880,
Tursiops truncatus	ENSTTRG00000004470	1 retrocopy	retro_ttru_249,
Vicugna pacos	ENSVPAG00000007016	5 retrocopies	retro_vpac_103, retro_vpac_203, retro_vpac_223, retro_vpac_490, retro_vpac_95,