RetrogeneDB ID: retro_lafr_774

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_37:21594369..21594678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSLAFG00000001987
• Aliases: None
• Description: None

Sequence

>retro_lafr_774
TGCAAAAAGCAAATTCTTCAAGGAAAATGAATATGAAAAAATCACCAAGAATACAATGCTTTAGCAAAAGTAATCCAGCA
TCATCCAGACAGGCATGAGACATTAAAGGAACTAGAGGCTTTGGGAAAAGAATTAGAGCATCTTTCACATGTTAAAGAAA
TTGTTGGAGATAAGCTGGAATTGAGGGGGAAACAGTTTCACGTTCTTCTTAGTACCATCCATGAACTTCAGCAAACACTG
GAAAATGATGAAAAACTCTCAGAGGTAGAAAAAGCTCAGGAAACAGGTGTGGAAACAGATCCTAAGCCA

Alignment

ORF - retro_lafr_774 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.35 %
• Parental protein coverage: 50.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLKELEALGKELEHLSHIKESVEDKLELRRKQFHVLL
          CKKQILQ.K.I.KN.QEY.ALAKVIQHHPDRHETLKELEALGKELEHLSH.KE.V.DKLELR.KQFHVLL
Retrocopy CKKQILQGK*I*KNHQEYNALAKVIQHHPDRHETLKELEALGKELEHLSHVKEIVGDKLELRGKQFHVLL

Parental  STIHELQQTLENDEKLSEVEEAQETSLETDPKP
          STIHELQQTLENDEKLSEVE.AQET..ETDPKP
Retrocopy STIHELQQTLENDEKLSEVEKAQETGVETDPKP

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_774 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 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585, retro_lafr_774 ,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,