RetrogeneDB ID: retro_lafr_519

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:105381774..105382584(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031572
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSLAFG00000014387
• Aliases: None
• Description: None

Sequence

>retro_lafr_519
TGGAATAGTGGATCTGAAAACTATGGCAGCTCCGCCTATGTTGGCGCTGGCGGCTACACAGTTCCCGGAGCGGGGGGCTT
TGGGTCGCCCACACCTACTCAAGCTGAAAAGAAATCAAGAGCCCGAGCCCAGCACATTGTACTCTGTACCGTATCCCGGC
TGCTTTCTGCCACCCTGGTTGACGAAGTGTTCAAAATTGGCAATGTTGAGATTTCACAGGTCGCAATCTTGGGGATAATC
AGACATGCAGAAAAGGCACCAACCAACATTGCTTACATATAGATGACATGACAGCTGCACCTATGGATGTTTGCCAGTGG
GTTGACACAGATGACCCAAGTGGTAAAAACGCTGTGGTTCCTCCAGAAACATATGTGAAAGTGGCCAGCCACCTGAGATC
TACTCAGAACAAAAAAAAGCCTGGTAACCTTCAAAACCATGCCCCTGGAGAATATGAATGAGTTCATCACACATATCCTG
GAAGCAGTCAATGCACACATGATGCTAAGCAAGTCTAACAACCAGCCTTCAGTAGGGAGAGCACCTATCAGCAATCCAGG
AATGGGTGAAGCAGGGAGCTTTGGTGAGAATAGCTTCATTCCTGTAAATGGCCTCACTGTAGCCCAAAACCAGGTGCTGA
ATTTGATCAAAGCTTGCCTAAGACCTGAAGGATTGAACTTTGATGATCTCAAGACTCAGCTCCAGTCCATGAGTGCAGTC
TCAATCAAGCAAGCTGTGGATTTTCTTAGCAACGAGGGACATACCTATTCCACTGTGGATAATGACTATTTTAAGTCCAC
AGACGGAGAA

Alignment

ORF - retro_lafr_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WNSGFENYGSSAYGGAGGYT-QSPGGFGSPTPTQAEKKSRARAQHIVPCTISQLLSATLVDEVFKIGNVE
          WNSG.ENYGSSAY.GAGGYT....GGFGSPTPTQAEKKSRARAQHIV.CT.S.LLSATLVDEVFKIGNVE
Retrocopy WNSGSENYGSSAYVGAGGYTVPGAGGFGSPTPTQAEKKSRARAQHIVLCTVSRLLSATLVDEVFKIGNVE

Parental  ISQVTIVGIIRHAEKAPTNIVY-KIDDMTAAPMDVRQWVDTDDPSGENTVVPPETYVKVAGHLRSFQNKK
          ISQV.I.GIIRHAEKAPTNI.Y..IDDMTAAPMDV.QWVDTDDPSG.N.VVPPETYVKVA.HLRS.QNKK
Retrocopy ISQVAILGIIRHAEKAPTNIAY<HIDDMTAAPMDVCQWVDTDDPSGKNAVVPPETYVKVASHLRSTQNKK

Parental  -SLVAFKIMPLEDMNEFTAHILEVVNAHMMLSKSNNQPSVGRAPISNPGMGEAGNFGANSFIPVNGLTVA
          .SLV.FK.MPLE.MNEF..HILE.VNAHMMLSKSNNQPSVGRAPISNPGMGEAG.FG.NSFIPVNGLTVA
Retrocopy >SLVTFKTMPLENMNEFITHILEAVNAHMMLSKSNNQPSVGRAPISNPGMGEAGSFGENSFIPVNGLTVA

Parental  QNQVLNLIKACPRPEGLNFDDLKTQLQYMSAVSIKQAVDFLSNEGHIYSTVDDDHFKSTDAE
          QNQVLNLIKAC.RPEGLNFDDLKTQLQ.MSAVSIKQAVDFLSNEGH.YSTVD.D.FKSTD.E
Retrocopy QNQVLNLIKACLRPEGLNFDDLKTQLQSMSAVSIKQAVDFLSNEGHTYSTVDNDYFKSTDGE

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_519 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 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519 ,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257, retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184, retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,