RetrogeneDB ID: retro_lafr_224

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:27346440..27347259(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028521
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT9
• Ensembl ID: ENSLAFG00000011391
• Aliases: None
• Description: None

Sequence

>retro_lafr_224
ATGGCTGGATGGCACCTGACAAAGGCTTTAACGATGGCATCTCTCTACGTGACTTTGGTCTCTGCGGCGATCAGGCTCAG
CAGCTGCCCCAGCATCCCTGCCAGCTGGAGACCATCTTCCTCATGTGGATTTCCTCTAAACATCATCATGTCAGGTTCAA
ATGGCGCTGCTGAGAACCTGCACAGGAAGTCCCGGACATCTCCGTATCCTGGTTCCAAAGTGAAGAGAAGCCACGTCCCC
AATGAGAAAGTGAGCTGGGAGGTTGAGTGGGGAGAGTACAACCCTGTTGAGTACACTGCCAGCTCTGTCTTGGCTGGGCC
CAGGTGGGCCGACCCCCAGGTGGGTGAAAAGAACTTCTCTCCTAAATTTAATGAAGAAGATGGGGATGTTGAGAGAAGGA
GCCAGAATGGTTGGTATAAGGTTGAAAATGGGAGACCTAGAAATCCTGTAGGTCGGACAGGGCTGGTTGGCCGAGGGCTT
TTGGGGCACTGGAGGCCCAATCATGCTGCAGATCCCATCATAACCAGATGTAAAAGGGATAGCAGGGGAAATAAAGTGCC
CCATCCTGTTTCTGGGAAAAACATCCTACAATTTGTAGCCATCAAAAGGAAGGACTGTGGAGAATGGGCAATCCCAGAGG
GGATGGTGGATCCAGGAGAGAAGATTAGTGCTGCACTGAAGAGAGAATTTGGTGAGGAGGCCACGAACTCCTTACAGAAA
TCCCAGGCGGAAACACAGGAGCTGGAGGAACAGCTGGACAAACTATTCAGCCAGGAAAATTTTGTGGTCTATAAAGGCTA
CGTGGATGATCCTCGGAAC

Alignment

ORF - retro_lafr_224 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.45 %
• Parental protein coverage: 78.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRVLGKALVTVSLSVALASVSVRSLGCRSIPAYRNSFSSCWFHLNPIIMSDSNGAKGKSHYKARTSPY
          MAG..L.KAL...SL.V.L.S...R...C.SIPA.....SSC.F.LN.IIMS.SNGA....H.K.RTSPY
Retrocopy MAGWHLTKALTMASLYVTLVSAAIRLSSCPSIPASWRPSSSCGFPLN-IIMSGSNGAAENLHRKSRTSPY

Parental  PGSKVERSQVPNEKVDWLVEWQEYNPVEYTAVSVLAGPTWADPQISESNFSPKFNEKDGHVQRKSQNGLY
          PGSKV.RS.VPNEKV.W.VEW.EYNPVEYTA.SVLAGP.WADPQ..E.NFSPKFNE.DG.V.R.SQNG.Y
Retrocopy PGSKVKRSHVPNEKVSWEVEWGEYNPVEYTASSVLAGPRWADPQVGEKNFSPKFNEEDGDVERRSQNGWY

Parental  EIENGRPRNPAGRTGLVGRGLLGRWGPNHAADPIITRWKRDSSGNKITNPVSGKNILQFVAIKRKDCGEW
          ..ENGRPRNP.GRTGLVGRGLLG.W.PNHAADPIITR.KRDS.GNK...PVSGKNILQFVAIKRKDCGEW
Retrocopy KVENGRPRNPVGRTGLVGRGLLGHWRPNHAADPIITRCKRDSRGNKVPHPVSGKNILQFVAIKRKDCGEW

Parental  AIPGGMVEPGEKISATLKREFGEEALNSLQKSNAEKRKIEEQLHQLFSQEHLVIYKGYVDDPRN
          AIP.GMV.PGEKISA.LKREFGEEA.NSLQKS.AE....EEQL..LFSQE..V.YKGYVDDPRN
Retrocopy AIPEGMVDPGEKISAALKREFGEEATNSLQKSQAETQELEEQLDKLFSQENFVVYKGYVDDPRN

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_224 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 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003244	1 retrocopy	retro_amel_612,
Bos taurus	ENSBTAG00000011354	1 retrocopy	retro_btau_1112,
Canis familiaris	ENSCAFG00000009529	1 retrocopy	retro_cfam_1271,
Callithrix jacchus	ENSCJAG00000006159	1 retrocopy	retro_cjac_1047,
Equus caballus	ENSECAG00000019556	1 retrocopy	retro_ecab_123,
Echinops telfairi	ENSETEG00000019164	1 retrocopy	retro_etel_348,
Felis catus	ENSFCAG00000003315	1 retrocopy	retro_fcat_1509,
Homo sapiens	ENSG00000170502	1 retrocopy	retro_hsap_709,
Gorilla gorilla	ENSGGOG00000014777	1 retrocopy	retro_ggor_602,
Loxodonta africana	ENSLAFG00000011391	1 retrocopy	retro_lafr_224 ,
Macropus eugenii	ENSMEUG00000012123	4 retrocopies	retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica	ENSMODG00000020738	2 retrocopies	retro_mdom_157, retro_mdom_706,
Mustela putorius furo	ENSMPUG00000002258	1 retrocopy	retro_mputfur_585,
Nomascus leucogenys	ENSNLEG00000009520	1 retrocopy	retro_nleu_464,
Oryctolagus cuniculus	ENSOCUG00000002670	2 retrocopies	retro_ocun_1045, retro_ocun_990,
Ochotona princeps	ENSOPRG00000004055	1 retrocopy	retro_opri_1152,
Pongo abelii	ENSPPYG00000014914	1 retrocopy	retro_pabe_613,
Pan troglodytes	ENSPTRG00000016259	1 retrocopy	retro_ptro_506,
Pteropus vampyrus	ENSPVAG00000004829	1 retrocopy	retro_pvam_475,
Sus scrofa	ENSSSCG00000009223	1 retrocopy	retro_sscr_447,
Tursiops truncatus	ENSTTRG00000004207	1 retrocopy	retro_ttru_1549,
Vicugna pacos	ENSVPAG00000004012	1 retrocopy	retro_vpac_125,