RetrogeneDB ID: retro_lafr_593

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:40600121..40601092(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC2
• Ensembl ID: ENSLAFG00000007414
• Aliases: None
• Description: None

Sequence

>retro_lafr_593
TGTCCTTCCCTCCCTTACTCACCCCACCTGCCCCCCTTCTGCTTCCCCTGCCCTAGGCAGCTGCCTCTATGATCCTGCTG
CGAGTGAACAACCACATCATCAAGGAGATGCTGGCGTTCAAGTTGGAGAACGTGGCCGCTGGAAACAAACCAGAAGCAGT
AGAAGTAACATTTGCAGACTTTGATGGGGTCCTCCATCGTATTTCAAAACCTAATGGAGACAAACAAAAATTATGGTCAG
TATTTATTTGAAATTCTATAAGGAACTTCAGGCATACAGTGCTGGTGAGTTATTCAAGAGGGTGTACGGAAGTTTCTTGG
TAAATCTAGAATCAGGATAAAAAGTCTGTTTGCTATATGGCCTTGAAAATCTTCCTGCCTCCAAAGATCTCATCATACAT
CAGGCTGTCACGTTGAAAGGAAATTGTTTTGCCTCTGTCTTTGAGAAATACTTCCAACTCCAAGAAGAGGGCAAGGAAGA
TGAGAACAGGGCAGTTATCCATTATAGGTGTGATGAGACCATGTCTCTTGAGTTCAAAAAGGACAGAGTTGCAGTAGTAT
TCAGCACAGTGTTCAAAGATGATGATGATGTGGTCATTGGAAAGGTGTTCATACAGGAATTCAGAGAAGGACGAAGAGCC
AGCCACACAGCCTCACAGGTCCTCTTTAGCCACACGGAACCTCCTCATGAGCTGAAAGACACTGAAACCGATGTCACTGT
GTGCGACAACATTGGCTATATCACTTCGTGCTAGTCCTTCGCCACAGAAACATCTGTGCCCAAGATGACACCATCAACTT
AATCCACACGTTTCGGGACTACCTGCATTACCACATGAAGTGCTCTAAGGCCTATATTCACACACTATGCAGGCGAAAAC
ATACGACTTCCTCAAGGTGCTGAACCGTGCACGCCCAGATGCCAAGAAAAAAGAAATGAAAATAATCACCGGGAACTTGT
TTTCATCCCGC

Alignment

ORF - retro_lafr_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 95.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CPSLLYP-SSPASFLLPLPGAAAAMILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHIS
          CPSL.Y....PA..LLPLP.AAA.MILL.VNN.II.E.LA.K.EN.AAGNKPEAVEVTFADFDGVL..IS
Retrocopy CPSLPYS<TPPAPLLLPLP*AAASMILLRVNNHIIKEMLAFKLENVAAGNKPEAVEVTFADFDGVLHRIS

Parental  NPNGDK-TKVMVSISLKFYKELQAHGADELLKRVYGSFLVNPESGYNVSLLYDLENLPASKDSIVHQAGM
          .PNGDK.TK.MVSI.LKFYKELQA..A.EL.KRVYGSFLVN.ESG..V.LLY.LENLPASKD.I.HQA..
Retrocopy KPNGDK<TKIMVSIYLKFYKELQAYSAGELFKRVYGSFLVNLESG*KVCLLYGLENLPASKDLIIHQAVT

Parental  LKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKVFMQEF
          LK.NCFASVFEKYFQ.QEEGKE.ENRAVIHYR.DETM..E.KKDRV.VVFSTVFKDDDDVVIGKVF.QEF
Retrocopy LKGNCFASVFEKYFQLQEEGKEDENRAVIHYRCDETMSLEFKKDRVAVVFSTVFKDDDDVVIGKVFIQEF

Parental  KEGRRASHTAPQVLFSHREPPLELKD--TDAAVGDNIGYIT-FVLFPRHTNTSARDNTINLIHTFRDYLH
          .EGRRASHTA.QVLFSH.EPP.ELKD..TD..V.DNIGYIT.FVL..RH.N..A.D.TINLIHTFRDYLH
Retrocopy REGRRASHTASQVLFSHTEPPHELKDTETDVTVCDNIGYIT<FVLVLRHRNICAQDDTINLIHTFRDYLH

Parental  YHIKCSKAYIHT-RMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR
          YH.KCSKAYIHT..M.AKT.DFLKVLNRARPDA.KKEMK.ITG..FSSR
Retrocopy YHMKCSKAYIHT<TMQAKTYDFLKVLNRARPDAKKKEMKIITGNLFSSR

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_593 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003197	2 retrocopies	retro_amel_1771, retro_amel_1846,
Canis familiaris	ENSCAFG00000014618	1 retrocopy	retro_cfam_513,
Choloepus hoffmanni	ENSCHOG00000010564	5 retrocopies	retro_chof_1845, retro_chof_2103, retro_chof_2226, retro_chof_2227, retro_chof_473,
Dasypus novemcinctus	ENSDNOG00000006037	1 retrocopy	retro_dnov_5,
Dipodomys ordii	ENSDORG00000016107	1 retrocopy	retro_dord_624,
Felis catus	ENSFCAG00000002370	1 retrocopy	retro_fcat_732,
Loxodonta africana	ENSLAFG00000007414	1 retrocopy	retro_lafr_593 ,
Myotis lucifugus	ENSMLUG00000004161	1 retrocopy	retro_mluc_390,
Mustela putorius furo	ENSMPUG00000016512	1 retrocopy	retro_mputfur_1294,
Mus musculus	ENSMUSG00000006304	1 retrocopy	retro_mmus_1556,
Oryctolagus cuniculus	ENSOCUG00000005516	1 retrocopy	retro_ocun_483,
Pteropus vampyrus	ENSPVAG00000017133	1 retrocopy	retro_pvam_1216,
Sorex araneus	ENSSARG00000003326	1 retrocopy	retro_sara_283,
Tarsius syrichta	ENSTSYG00000001037	1 retrocopy	retro_tsyr_557,