RetrogeneDB ID: retro_lafr_734

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_34:21845359..21845803(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSLAFG00000012658
• Aliases: None
• Description: None

Sequence

>retro_lafr_734
TGTGACTCCACTGATGACCAGGCTACAGAGTTAAAGGAGCCCTTCCAGCTGTTTGCCCAACGGGTGATGGCAAGATCCTG
TACAGCCAGTGTAGGGACGTGATGAGGGCCCTGGGCAGAGCCCCACCAACGCCTAGGTGCTCAAGATCCTGGGGAACCCC
AAGAGTGATGAGATAAATGTGAAGGTGCTGGATTTTGAGCACTTTCAGTCTATGCTACAGACTGTGGCCAAGAACAAGGA
CCAGGGCACCCATGAGAACTATGTCGAAGGCCTTGGGTGTTTGACGAGGAAGGGAATGGCACCATCATGAGTGCTGAAAT
TTGGCATGTCCCTGTCACACTGGGTGAGAAAAAGATGAAGGAAGAATAGAGATGCTAGTGGCAGGGCACAAGGACAGCAA
TTGGTTGTATCAATTGTGAAGAGCTCATCCGTATGCTGCTGAAT

Alignment

ORF - retro_lafr_734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.62 %
• Parental protein coverage: 98.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  CDFTEDQTAEFKEAFQLFDR-TGDGKILYSQCGDVMRALG-QNPTNAEVLKVLGNPKSDEMNVKVLDFEH
          CD.T.DQ..E.KE.FQLF...TGDGKILYSQC.DVMRALG.Q.PTNA.VLK.LGNPKSDE.NVKVLDFEH
Retrocopy CDSTDDQATELKEPFQLFAQ<TGDGKILYSQCRDVMRALG<QSPTNA*VLKILGNPKSDEINVKVLDFEH

Parental  FLPMLQTVAKNKDQGTYEDYVEGLR-VFDKEGNGTVMGAEIRHVLVTLGEKMTEEE-VEMLVAGHEDSN-
          F..MLQTVAKNKDQGT.E.YVEGL..VFD.EGNGT.M.AEI.HV.VTLGEK...EE..EMLVAGH.DSN.
Retrocopy FQSMLQTVAKNKDQGTHENYVEGLG<VFDEEGNGTIMSAEIWHVPVTLGEKKMKEE<IEMLVAGHKDSN>

Parental  GCINYEELVRMVLN
          GCIN.EEL.RM.LN
Retrocopy GCINCEELIRMLLN

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_734 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734 ,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,