RetrogeneDB ID: retro_lafr_791

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_39:3674676..3676950(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SMEK2
• Ensembl ID: ENSLAFG00000017825
• Aliases: None
• Description: None

Sequence

>retro_lafr_791
ATGGCGCTCAGGCGGCGCCGTGTCAAAGTCTATATCCTGAACGATCACCGGGAATGGGACGACCTAGGCACCGGGTTGAT
CTCATCTACTTACGTGGGGCGGCTGCAGGGAGTGTCCCTGCTAGTTCGTTCCGAGTGCAACGGCTCCCTAATCTGGGAGT
CGAAGATAAATACACACACACGGTATCAGAAACAACAGGAGTCATTGATTGTTTGGTCGGAAGCCGAGAACCACGGTCTG
GCGCTAAGTTTCCAGGAACGAGCCGGCTGTCAGGCAATCTGGAAGGACATTTGCCGCGTTCAAGGTAAAGACCCCTCCGC
CGAAATCACACAAGACCTTTTGGATGAATCAGAAGAGGAACAATTTGATGAAATACCAGACACCAGTAATCTGGTTGTCC
TGCCTAATTGTGAACTCAACAATCTTGAACAGATTGCTGGCTTAGTTAACACAGTTCTTGCCTCGCCTATCCGTAGGGAA
AGGCTGGCTCTGATCTTGGAAAATGAGAACTATATTAAAAAACTACTGCAGTTGTTCCACACTTGTGAGACGCTAGAGAA
CACCGAAGGCTTGCACCATTTGCATGCCATTATTAAAGGAATCTTATTCCTCAACAAGACATCTCTGTTTGAGATCATGT
TTTCTGATGAATGCATCATGGATGTGGTGGGATGCCTTGAATACGACCCTGCTTTGGCTCAGCCTAAAAGGCATAGGGAA
TTCTTGACCCAAGTTGCAAAGTTCAAGGAAGTTATACCAATAACAGACTGTGAACTTAAGCAAAAAATACGTCAGACCCA
CAGGCTACAGTACATTCACGATATCTTATTGCCTATACCATCCATGTTTGAAGAGAATATGCTTTCTGCTCTTACTACTT
GTATTTTCTTCAACAAAGTTGAGATAGTCAACTTACTGCAGAACAATGACAAGTTTTTGTCTGAGGTTTTTGCACAGTTA
ACAGCTAAGACCACAGCTGATGATCAACTGCGTGAATTGGTGTTTTTTTTAAAGGAATTCTGTGCATTTTCTCAGACCTT
ACAACCACAAAGCAAGGATGCATTATTCCAAAAGTTCACAAGATTGGGAATTCTTCCTGCTCTTAAAAGTGTCATAGGCA
TGGACAATCTGCAGATAAGGTCAGCTGCTACAGATATATTTGTCTATCTAGTGGAGCGTAGTCCATCCATGATCCGACGA
TTTATAATGGACGAAGCCCTGCTCTGCAAAGATGGTAACCTTTTAATTACTATAATAATTGAACAAATGATCGGTGATAC
TGACCCTGAGCTAGGAGGTGCTGTTCAATTAATGGGGCTTCTTCGTTCTTTACTTGATCCAGACAACATGCTGGCTGTAC
CTAGTGAAAGACAAAGAAGTGAATTTCTAAATTTCTTCTACAAACGTTGCATGCATGTCTTGATAGGGCCACTTTTGGCC
AGCACTTCAGAAGACAAATGTGAAAAGGATAATACAGGTGGAGCTAGCAAAAATTGCCCCGATAATTATCAGACAGCACA
ACTGCTTGCCATAATTTTAGAGCTGCTCACGTTTTGTGTACAACATCACGCATATTACATAAAAAATTATATTTTGAACA
AAGACTTGCTAAGAAGAATCTTGATCCTGATGAACTCAAAGCACACTTTCCTGATCTTGTGTGCTGTTCGCTTTATGAGA
AGGATGATTGGCCGTAAAGATGAACTTTATAATTGTTACATCATCAAGGGAAATCTTTTTGAGCCAGTCATAAATGCTCT
TCTGAATAACGGGACTCGGTACAATATGTTGAATTCAGCTGTAATTGAGCTGTTTGAATACATAAGAGTGGAAAATATTA
AGTCTCTTGTTGCACATATAGTTGAGAAGTTTTATAAGGCAGTTGAATCGATTGAATATGTTCAGACATTCAAAGGACTG
AAGATTAAATATGAACAAGAGAAAGAGAGACAAAGTCAAGTACAGAAGAATTTGCATCCTATACTGCCTAGCAAAATACT
TTATGAAGGTGCCAATGTCTTTGAGGAGATAGAAGAAGTGAGTTTTAAGGAAGATAAAGAGGAAGGAGGAGCAATTATGC
CGCCATTGGAAACTCCTGCGCCAAAAGACCACTTTCCAAATCATTGTGGTAACATGACGGAGATTGAAAAAAGAAAAGTC
AATGCAGACAAGACCAACCTTCAGGAAAAAGCATCTGGTGACTTCAAATTTACTCCATCGCTTTCTGCCGGTGTTGCTAA
TGGAACAAGTAGTCCAGATGGTAGCAGTGTGGTT

Alignment

ORF - retro_lafr_791 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 93.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQARDT
          M...RRRVKVY.LN..R.WDD.GTG..SSTYV..L.G.SLLVR.E..GSL..ESKIN..T.YQKQQ....
Retrocopy MALRRRRVKVYILNDHREWDDLGTGLISSTYVGRLQGVSLLVRSECNGSLIWESKINTHTRYQKQQ--ES

Parental  LIVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCE
          LIVWSEAEN..LALSFQE.AGC..IW..IC.VQGKDPS.E.TQDL.DESEEE.F.E.P.TS.L..LP.CE
Retrocopy LIVWSEAENHGLALSFQERAGCQAIWKDICRVQGKDPSAEITQDLLDESEEEQFDEIPDTSNLVVLPNCE

Parental  LNKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKAT
          LN.LE.IA.LV..VL.SPIRRE.LAL.LENE.YIKKLLQLF..CE.LENTEGLHHL..II.GILFLNK..
Retrocopy LNNLEQIAGLVNTVLASPIRRERLALILENENYIKKLLQLFHTCETLENTEGLHHLHAIIKGILFLNKTS

Parental  LFEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILP
          LFE.MFSDECIMDVVGCLEYDPALAQPKRHREFLT..AKFKEVIPITD.EL.QKI.QT.R.QYI.DI.LP
Retrocopy LFEIMFSDECIMDVVGCLEYDPALAQPKRHREFLTQVAKFKEVIPITDCELKQKIRQTHRLQYIHDILLP

Parental  TPSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQ
          .PS.FEEN.LS.LT..IFFNKVEIV..LQ...KFLSEVFAQLT...T.DD..RELV.F.KEFCAFSQTLQ
Retrocopy IPSMFEENMLSALTTCIFFNKVEIVNLLQNNDKFLSEVFAQLTAKTTADDQLRELVFFLKEFCAFSQTLQ

Parental  PQNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINV
          PQ..DA.F.....LGILPAL..V.GMD.LQ.RSAATDIF.YLVE.SPSM.R.F.M.EA....D..LLI..
Retrocopy PQSKDALFQKFTRLGILPALKSVIGMDNLQIRSAATDIFVYLVERSPSMIRRFIMDEALLCKDGNLLITI

Parental  IIEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLANTSEDKYE
          IIEQMI.DTDPELGGAVQLMGLLR.L.DP.NMLA.......SEFLNFFY..CMHVL..PLLA.TSEDK.E
Retrocopy IIEQMIGDTDPELGGAVQLMGLLRSLLDPDNMLAVPSERQRSEFLNFFYKRCMHVLIGPLLASTSEDKCE

Parental  KDNIVGSNKNNTVCPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCA
          KDN..G..KN...CPDNYQTAQLLA.ILELLTFCV.HH.Y.IKNYI.NKDLLRR.L.LMNSKHTFL.LCA
Retrocopy KDNTGGASKN---CPDNYQTAQLLAIILELLTFCVQHHAYYIKNYILNKDLLRRILILMNSKHTFLILCA

Parental  LRFMRRIIGLKDEFYNRYITKGNLFEPVVNALLDNGTRYNLLNSAVVELFEFIRVEDIKSLTAHIVENFY
          .RFMRR.IG.KDE.YN.YI.KGNLFEPV.NALL.NGTRYN.LNSAV.ELFE.IRVE.IKSL.AHIVE.FY
Retrocopy VRFMRRMIGRKDELYNCYIIKGNLFEPVINALLNNGTRYNMLNSAVIELFEYIRVENIKSLVAHIVEKFY

Parental  KALESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRSNRFRRDAKALEEDEEMWFNEDEEEEGKAVVA
          KA.ESIEYVQTFKGLK.KYEQEK.RQ.Q.......IL.S......A...EE.EE..F.ED..EEG.A...
Retrocopy KAVESIEYVQTFKGLKIKYEQEKERQSQVQKNLHPILPSKILYEGANVFEEIEEVSFKED-KEEGGAIMP

Parental  PVEKSKPEDDFPDSYEKFMETKKAKESEDKENLPKRTSSGGFKFTFSHSASAANGTNSANSKSVV
          P.E...P.D.FP.......E..K.K...DK.NL.....SG.FKFT.S.SA..ANGT.S....SVV
Retrocopy PLETPAPKDHFPNHCGNMTEIEKRKVNADKTNLQEK-ASGDFKFTPSLSAGVANGTSSPDGSSVV

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_791 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 18 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003843	1 retrocopy	retro_amel_48,
Bos taurus	ENSBTAG00000000545	1 retrocopy	retro_btau_232,
Canis familiaris	ENSCAFG00000002860	1 retrocopy	retro_cfam_226,
Equus caballus	ENSECAG00000013819	1 retrocopy	retro_ecab_23,
Echinops telfairi	ENSETEG00000002420	1 retrocopy	retro_etel_1699,
Felis catus	ENSFCAG00000026457	1 retrocopy	retro_fcat_13,
Homo sapiens	ENSG00000138041	1 retrocopy	retro_hsap_4799,
Loxodonta africana	ENSLAFG00000017825	1 retrocopy	retro_lafr_791 ,
Myotis lucifugus	ENSMLUG00000003875	1 retrocopy	retro_mluc_994,
Macaca mulatta	ENSMMUG00000007001	1 retrocopy	retro_mmul_238,
Mustela putorius furo	ENSMPUG00000002435	1 retrocopy	retro_mputfur_92,
Nomascus leucogenys	ENSNLEG00000009338	1 retrocopy	retro_nleu_1112,
Oryctolagus cuniculus	ENSOCUG00000006880	1 retrocopy	retro_ocun_9,
Otolemur garnettii	ENSOGAG00000009837	1 retrocopy	retro_ogar_140,
Pan troglodytes	ENSPTRG00000011933	1 retrocopy	retro_ptro_3191,
Sus scrofa	ENSSSCG00000008398	1 retrocopy	retro_sscr_1187,
Ictidomys tridecemlineatus	ENSSTOG00000006276	1 retrocopy	retro_itri_63,
Tursiops truncatus	ENSTTRG00000000027	1 retrocopy	retro_ttru_1397,