RetrogeneDB ID: retro_lafr_370

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:8240750..8241029(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSTB
• Ensembl ID: ENSLAFG00000002664
• Aliases: None
• Description: None

Sequence

>retro_lafr_370
GCCATGCAGCCGCCCACAACCGAGGCCCAGGAGACCCTGGAGATTGCCAACCAGGTAAAGCCTCAGCTTGAAGAGAAAGA
ATATAAGATGTTCCCGATGTTTAAGGCTGTGGAGTCCAAGAGGCAGGTGGTCACCGGAACAAAGGACTTTATCAGGATTC
ATGTAGGTGACAAAAACTTTGTGCACCTTCAAGTATTTCAGAGTCTTCCTCACAAAACAAGCCCGACTTTGTCCAGCTAC
TAGAGCAACAAGGTCAAGCATGACAAGTTGGAATATTAC

Alignment

ORF - retro_lafr_370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATQPATAETQ---EIADKVKAQLEEKENKKFPVFKAVEFKSQVVAGTNYFIKVHVGNDNFVHLRVFQSLP
          A.QP.T.E.Q...EIA..VK.QLEEKE.K.FP.FKAVE.K.QVV.GT..FI..HVG..NFVHL.VFQSLP
Retrocopy AMQPPTTEAQETLEIANQVKPQLEEKEYKMFPMFKAVESKRQVVTGTKDFIRIHVGDKNFVHLQVFQSLP

Parental  HEDKPPALTSYQTNKAKHDELTYF
          H....P.L.SY..NK.KHD.L.Y.
Retrocopy HKTS-PTLSSY*SNKVKHDKLEYY

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_370 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000524	1 retrocopy	retro_btau_97,
Loxodonta africana	ENSLAFG00000002664	1 retrocopy	retro_lafr_370 ,
Myotis lucifugus	ENSMLUG00000022457	1 retrocopy	retro_mluc_379,
Macaca mulatta	ENSMMUG00000012303	1 retrocopy	retro_mmul_1609,
Otolemur garnettii	ENSOGAG00000006101	2 retrocopies	retro_ogar_3274, retro_ogar_3275,
Pteropus vampyrus	ENSPVAG00000007022	1 retrocopy	retro_pvam_1089,
Rattus norvegicus	ENSRNOG00000001201	1 retrocopy	retro_rnor_551,
Sarcophilus harrisii	ENSSHAG00000017952	3 retrocopies	retro_shar_229, retro_shar_623, retro_shar_699,