RetrogeneDB ID: retro_lafr_1146

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_78:7568875..7572496(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000023062
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HDLBP
• Ensembl ID: ENSLAFG00000014826
• Aliases: None
• Description: None

Sequence

>retro_lafr_1146
ATGAACTCTGAAGAAAATTCGACTGAAGAAAGCACTGCTAAGCACCAGAGCAAGTACATTCAGAAAGAAAACTATGTTAC
TGCTTTAAATTCAGAAGAGGTGCTCGGCACTCCAATCTACACAGACAAAGCCCCTCAACTCCTAGACAAAACAAATTCAC
TGGAAAATCCTCAGGAACCTGCTGGATCCTCCAGCAGTAATATTCAACCTAGCAATTCAACCTCAGTCGTCTCTCAAATT
GTTTATGTGCCTCTGGAGGAAAGAAAGTATTTAAATCAGTTTGGTGAGGGTAGACAAGCCAAATTCTTTATAGATATCAT
GCACAGGACTGGTGCCAACCTGGAAGAATTAACTTTTATCAAAGACCAAGGTCTCTACATTATAGTCTCTGGTAAGCCAG
AAACTGTTAAGAAAGCCCAGAAGGAGATTTTTGCTTGGTTTCACGAACAAGATTCAACCACCGTTTCCGCTTTCAAAGAA
CAATGTTGCACTGTTATAGGCAAGACTGGAGAAAAACTACAAAACTTGGAAGAAAACACGGCAACCAACATCCAGATTCT
ATGCCCTGATAACTATCAAAACCGAATCAAGATTGCTGGCACCAAAGAGGGCATAAAGAAATATCCACACGAAGTTTTTA
CGTCTGAGGAACAAGACAAGCATGCTTCAGAGAGGCTAGATATGGAAATGTTATTTCATCCTTCTGTTGCCAGGCCATAC
AATACATCTGTTTACAAAGTCGTGCAGGAGGAAGAGGCACGCATACGTATTCCACCACCTAGTACCAATCACACAGAGGT
AATGTTTACTGAAAAAAAGCAACAGCTAAATCAGTCTGTGGCTCCTGTAAAGGAGAGTTTTGAGGATACCAAAAAGAAAA
ATATAGCCACAGCTATGGAGATGAAATTGCAGCACAAGTGTACTATTGGGCCCAAGATCAATTCTGTGCAGGAAATCCTG
GAAAGAACTGGAGTTTCAATCGAGATTTCACCCTCGGAGAACATGTCAGATCCTGAGACACTCCAAGGTGAGCCTGAAAG
TTCAGGGAAGGCATTTACTAAAGTGTGTTCAAAGTCCAAGCGTTACACTGTTTCCTCAGTTTCTGCACCTTCCTGGATTC
ACAGATTTATCATTGGTAAAAAAGGTCAAAATATAGCCACAATAACTGAGAATAGGCCAAAAGTTTGTGTAGAATTTACT
GGAGATGATAAAATTATCATAAAAGGACCTACAAAAGATGTGAATTATATTCGAGACAAAATTGAGGTCATAGTCAAAGA
CCTAATTGACAGGATGTATTATGAAGAGATTAATATTGACTACAAGGTTCACAAATATCTGATAGGGAAGAATGGTGTCA
CCATAAACCAGATTAAAGAGAAGAATAAAGTTTCTGTGCTAATCTCACCCGAAAATGCAAAGAATAACTTGATCAGAATT
GAAGGGGAAGCTTGGGGTGTCCAACAGGCCAAGAGAGAACTTCTGGAGCTTGCTGCTCATGCGAAAAATGAGCAGAGCAA
AGACTTAATTATCGAGCAAAGATTTCATCGCACAATCATTGGGCAGAAAGGTGAACGGATTCGTGATATCCGTAAGAAAT
TCCCAGAAGTTATGATTAATTTTCCTGATCTAGCACAAAAAAGTGACATTGTCCAACTCAGAGGGCCCAAGTATGAATTA
GAACAGTGCACAGAATATTTGGAGAATGTGGTGACAGACCTTGTAGAAAACAACTATTCCATTACTATTCCCATATTCAA
AAAGCTTCACAAGAATATAATCGGAAAAGGAGGTGCAAACATCAAAAAAATCTGTGCAGCGAGCAACACCAAAATTCAGC
TTCCATCAGCAGGTAGCAACTCAGAGAATATTGTCATCACTGGGAAACGGGAAAACTGTGAAGTAGCGTATAACTGGATT
CTTTCCATTCAGAAAGATACAGCCAATATTTCAGAAACAGAAATTTCTATTCCTTCTGATCTACATATAGCCCTTATAGA
TCCCAAAAGCTGTTTGATTGGTTCAATCATGGAAGAATGTGGAGGGATCTGCATGCACTTTCCAAAAGACAACTCAGGTC
TTCAAAGGGTCATCATTAAGGGCCCTACCCAAAGTGTTGAGAAGGCTAAGAAAAAGCTGCTGCAACTAGCAGAAGAAAAA
GAAAGCAAGAGTTATGCTGTGGTCCTCCAGGTCAAACCACAGTATCACAAATTTCTCATGAGTAAAAATGGTGGCAATGT
TCCTAAAATCTGTGATGAGACTGGAGCACATATCGTCTTCCCACTCCCTGAGGATGAGAATCAAGAACTGATAACTATTA
CTGGAATAGAAGAGGCTGTTAAAGATGCACAAAAGGAACTAGAAGCTCTAATCCAAAACCTAGACAGTGTTGTAGAGGAC
AATATACTGATAAATCCCAAGTACCACCGTCACTTTATCATGAGAAGGGGCCAGGTTTTACGGGAGATAACCGAGGAGTG
TGGTGGTGTGATTATTAATATTTCATGTTCAGGAAAAAAGAACAATAAAGTCACAATCAAAGGAGCAAAACCTTGCGTGG
AAGCAGCCAAAAAACAGATCCAGGAAATTATTGGCGACTTTCATACCCAAGTCACAACAGAATGTGTTATTCCCCAGAAA
TTCCATCATTTTGTCCTGGGACCAATGTGTTCCCGAGTCCGACAAATCAGTAGGGATTATAATGTTCGAATCAAATTTCC
AGACAGAGAGGAGAATGTAGTTACTAATACAGAGCCAGTTGTTCAGGAAGGTGAAGACAAAATTGGGAAAAGGAACACAA
AGGAGGGTAATCCTATTTTTCCAAGGAAATGTGACACCATATATATATCAGGTCGAAAGGAAAAGTGTGAAGCAGCCATG
GAAGCCCTTGTGGCTTTAATTCCTGTTACTGTTGAAGTAGATGTGCCCTTTGACCTTCACCGTTACATCATTGGTCAGAA
AGGAAGTGGCATACGTAAGTTGATGGAGGAGTTTGAAGTTGATATACAAGTCTCAGCAGCTGAATTACAGTCCAGTAGTG
TTTCCATCACTGGCCTTGCTGCAAATGTCAAACAAGCCAAAGCTAGATTAGAAGAACGAGTCGTAGCTTTACAAGCTGAA
ATACAAGATCGAGCATTAAGAAATTTTAAACTGAGCTTAACCGTAGACCCCAAATACCACCCCAAGATCATTGGTCAAAA
GGGTTTAGTTATTGCTCAGATTTGCTTAGAACATGAAGTTACCATCCATTTTCCAAGTAAAGAGAGCAATGAAACACAAG
ACCAAATCATTATCACTGGATATGAGAAAAATACCATTGCTGCCCGCGATGCAATAATGAAAATGGTGCATAAGTTTGAA
AAAACAATAACTAGGAAAACCCCACTAAACCACCGTGTTCATGGCCAAATTATTGGGTTCCGTGGGAAGGCCATTAATAA
AATCATGAATCAATTCCAAGTAGATATCCGTTTCCCTCCCAGGGAGGCCCCAGATCCCAAACTTTGTCACTGTGACTGGA
GTTCGTGATAAAGTCACAAAAGCAATTGATCATATCCTTAGTCTTGAGGACATTATCTGGCTACTGCCATAAAGCATGAG
TCTCAGCAAGAGCATATGAAG

Alignment

ORF - retro_lafr_1146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.09 %
• Parental protein coverage: 95.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSVAVLTQESFAEHRSGLIPQQIKVATLNSEEESDPPTYKDAFPPLPEKAACLENAQEPAGAWSNKIRP
          M.S....T.ES.A.H.S..I.....V..LNSEE....P.Y.D..P.L..K...LEN.QEPAG..S..I.P
Retrocopy MNSEENSTEESTAKHQSKYIQKENYVTALNSEEVLGTPIYTDKAPQLLDKTNSLENPQEPAGSSSSNIQP

Parental  IKA-SVITQVFHVPLEERKYKDMNQFGEGEQAKICLEIMQRTGAHLE-LSLAKDQGLSIMVSGKLDAVMK
          ....SV..Q...VPLEERKY...NQFGEG.QAK....IM.RTGA.LE.L...KDQGL.I.VSGK...V.K
Retrocopy SNSTSVVSQIVYVPLEERKY--LNQFGEGRQAKFFIDIMHRTGANLEELTFIKDQGLYIIVSGKPETVKK

Parental  ARKDIVARLQTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKA
          A.K.I.A....Q.S.TV...KE....VIGK.GEKLQ.LE..TAT.IQI..PD...N.IKI.GTKEGI.K.
Retrocopy AQKEIFAWFHEQDSTTVSAFKEQCCTVIGKTGEKLQNLEENTATNIQILCPDNYQNRIKIAGTKEGIKKY

Parental  RHEVLLISAEQDKRAVERLEVEKAFHPFIAGPYNRLVGEIMQETGTRINIPPPSVSRTEIVFTGEKEQLA
          .HEV...S.EQDK.A.ERL..E..FHP..A.PYN..V....QE...RI.IPPPS...TE..FT..K.QL.
Retrocopy PHEVFT-SEEQDKHASERLDMEMLFHPSVARPYNTSVYKVVQEEEARIRIPPPSTNHTEVMFTEKKQQLN

Parental  QAVARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSASETVILRGEPE
          Q.VA..K...E..KKK....A.E.K..QHK..IGPK.NS.QEILERTGVS.EI.PS...S....L.GEPE
Retrocopy QSVAPVKESFEDTKKKNIATAMEMKL-QHKCTIGPKINSVQEILERTGVSIEISPSENMSDPETLQGEPE

Parental  KLGQALTEVYAKANSFTVSSVSAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDVN
          ..G.A.T.V..K....TVSSVSAPSW.HRFIIGKKGQN.A.IT...PKV..EFT.G.DKI...GPT.DVN
Retrocopy SSGKAFTKVCSKSKRYTVSSVSAPSWIHRFIIGKKGQNIATITENRPKVCVEFT-GDDKIIIKGPTKDVN

Parental  VAQGQIEAMVKDLVNRMDYVEINIDHKFHRHLIGKSGSNINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQ
          .....IE..VKDL..RM.Y.EINID.K.H..LIGK.G..IN.IK...KVSV.I.P...K.NLIRIEG...
Retrocopy YIRDKIEVIVKDLIDRMYYEEINIDYKVHKYLIGKNGVTINQIKEKNKVSVLISPENAKNNLIRIEGEAW

Parental  GVQQAKRELLELASRMENERTKDLIIEQRFHRTIIGQKGERIREIRDKFPEVIINFPDPAQKSDIVQLRG
          GVQQAKRELLELA....NE..KDLIIEQRFHRTIIGQKGERIR.IR.KFPEV.INFPD.AQKSDIVQLRG
Retrocopy GVQQAKRELLELAAHAKNEQSKDLIIEQRFHRTIIGQKGERIRDIRKKFPEVMINFPDLAQKSDIVQLRG

Parental  PKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNSETII
          PK.E.E.CT.Y....V.DLVEN.YSI..PIFK..HKNIIGKGGANIKKI...SNTKI.LP...SNSE.I.
Retrocopy PKYELEQCTEYLENVVTDLVENNYSITIPIFKKLHKNIIGKGGANIKKICAASNTKIQLPSAGSNSENIV

Parental  ITGKRANCEAARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSD
          ITGKR.NCE.A...ILSIQKD.ANI.E.E.SIP..LH..LI..K..LI.SIMEECGG...HFP...SG..
Retrocopy ITGKRENCEVAYNWILSIQKDTANISETEISIPSDLHIALIDPKSCLIGSIMEECGGICMHFPKDNSGLQ

Parental  TVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGTRIIFPAAED
          .V.I.GP...VEKAKK.LL.LAEEK..KS..V....KP.YHKFL..K.GG...K..D.TG..I.FP..ED
Retrocopy RVIIKGPTQSVEKAKKKLLQLAEEKESKSYAVVLQVKPQYHKFLMSKNGGNVPKICDETGAHIVFPLPED

Parental  KDQDLITIIGKEDAVKEAQKELEALIQNLDNVVEDYMVVDPRHHRHFVIRRGQVLREIAEEYGGVMVSFP
          ..Q.LITI.G.E.AVK.AQKELEALIQNLD.VVED.....P..HRHF..RRGQVLREI.EE.GGV.....
Retrocopy ENQELITITGIEEAVKDAQKELEALIQNLDSVVEDNILINPKYHRHFIMRRGQVLREITEECGGVIINIS

Parental  RSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTMECAIPQKFHRSVMGPKGSRIQQITRDYGVQIK
          .SG....KVT.KGAK.CVEAAKK.IQEII.D...QVT.EC.IPQKFH..V.GP..SR..QI.RDY.V.IK
Retrocopy CSGKKNNKVTIKGAKPCVEAAKKQIQEIIGDFHTQVTTECVIPQKFHHFVLGPMCSRVRQISRDYNVRIK

Parental  FPDREENPVHSVEPAMQENGDETAEGRDTKEADPGSPRRCDIIVISGRKEKCEAAKEALEALVPVTTEVE
          FPDREEN.V...EP..QE..D.....R.TKE..P..PR.CD.I.ISGRKEKCEAA.EAL.AL.PVT.EV.
Retrocopy FPDREENVVTNTEPVVQEGEDKIGK-RNTKEGNPIFPRKCDTIYISGRKEKCEAAMEALVALIPVTVEVD

Parental  VPFDLHRYIIGQKGSGIRKMMDEFEVNIQVPAPELQSDIIAITGLAANLDRAKAGLLERVRELQAEQEDR
          VPFDLHRYIIGQKGSGIRK.M.EFEV.IQV.A.ELQS....ITGLAAN...AKA.L.ERV..LQAE..DR
Retrocopy VPFDLHRYIIGQKGSGIRKLMEEFEVDIQVSAAELQSSSVSITGLAANVKQAKARLEERVVALQAEIQDR

Parental  ALRSFKLSVTVDPRYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGSQPQDQITITGYEKNTEAARDAIL
          ALR.FKLS.TVDP.YHPKIIG.KG.VI.QI.LEH.V.I.FP.K......QDQI.ITGYEKNT.AARDAI.
Retrocopy ALRNFKLSLTVDPKYHPKIIGQKGLVIAQICLEHEVTIHFPSK-ESNETQDQIIITGYEKNTIAARDAIM

Parental  KIVGELEQMVSEDVPLDHRVHARIIGARGKAIRKVMDEFKVDIRFPQSGAPD-PNCVTVTGLPENVEEAI
          K.V...E.......PL.HRVH..IIG.RGKAI.K.M..F.VDIRFP...APD.PN.VTVTG....V..AI
Retrocopy KMVHKFEKTITRKTPLNHRVHGQIIGFRGKAINKIMNQFQVDIRFPPREAPD>PNFVTVTGVRDKVTKAI

Parental  DHILNLEE-EYLADVVDNESLQVYMK
          DHIL.LE...YLA.....ES.Q..MK
Retrocopy DHILSLED<HYLATAIKHESQQEHMK

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_1146 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012829	1 retrocopy	retro_ecab_1042,
Loxodonta africana	ENSLAFG00000014826	1 retrocopy	retro_lafr_1146 ,
Mus musculus	ENSMUSG00000034088	1 retrocopy	retro_mmus_194,
Nomascus leucogenys	ENSNLEG00000013818	1 retrocopy	retro_nleu_1292,
Pongo abelii	ENSPPYG00000013351	1 retrocopy	retro_pabe_1544,