RetrogeneDB ID: retro_lafr_446

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:3236273..3238056(+)
• Located in intron of: ENSLAFG00000011894

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSLAFG00000015777
• Aliases: None
• Description: None

Sequence

>retro_lafr_446
TATCTCTACTTGATGAACTATGTCAGGAGTCAGCCAGACATGGCCATCATGGCTGTCAACTGTTTGTGAAGGACTGTGAA
GACCCCCATCCATTGATTCGAGCCTTGGCAGTCAGAACCATGGGCTGCATCTGGGTAGACAAGATTACAGAATCTCTCTG
TGAGCCCCTCCGCAAGTGCTTGAAGGATGAAGACTCCTATGGTCAGAAAACTGCTGTGGTCTGCATGGCAAAGTTCCATG
ATATCAATACCCAAATGGTGGAAGATCAGGGATTCCTGGATTCTCTGTGAGATCTCATAGCAGATTCAAATCCAATGGTG
GTGGCCAGTGCTGTAGCAGCGTTATCTGAAATCAGCAAGGCTCACCCAACAGCAATCTACTTAATCCAAACCCACAGAAC
ATTAATAAGCTGCTGACAGCCCTGAATGAGTGCACTGAATAGGGCCAGATTTTCATCCTTGACTGCCTATCTAACTAAAA
CCCTAAAGACAACCGGGGGGCTCAGACCATCTGTGAGCAGGTAACTCCCTGGCTATCCCATGCCAACGCAGCAGTGGTGC
TCTCGGCAGTAAAAGTCCTAATGAAATTTCTAGAGTTGTTACCCAAGGACTCTGACTACTACAATATGCTGCTGAAGAAG
TTAGACCCTCCACTTGTCATTTTGCTGTCTGGGGAGGCAGAGGTGCAGTATGCCGCCTTGAGGAACATCAACCTAATTGT
CCAGGAAAGGCTTGAAATCTTGAAGCAGGAAATCAGTGTCTTCCTAGTGAAGTACAACGATCCCATCTATGTTAAACTAG
AGAAGTTGGACATCATGATTCGTTTGGCATCCCAAGCCAACACTGCACAGGTTTTGAAGAACTGAAGGAATATGCCACAG
AGGTGGATGTTGACTTTGTTCGCAAAGCTGTGCAGGCCATGGATGGTGTGCCATCAAGGTGGAGCAATCTGCAGAGCGCT
GTGTAAGCACATTGCTTGATCTCATCCAGACAAAAGTAAATTATGTGGTCCAAGAGGCAACTGTTGTCATCCAGGACATC
TTCCTCAAGTATCCCAATAAGTATGAAGGTACCATTGCTACTCTATGTGAGAACTTAGACTGGCTCGATGAGCCAGATGC
TCGAGCAGCTATGATTTGGATCGTGGGAGAATATGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAGAGCTTCCTAG
AGGGTTTTCATGATGAAACCACCCAGGTGCAGCTTACTCTGCTTACTGCCATAGTGAAGTTGTTTCTTAAGAAATCATCA
GAAACACAGGAACTGGTCCAGCAAGTCTTGAGTTTGGCAACCCAGGATTCTGGTAACCCTGACCTTCGAGACCGAGGCTA
TATTTACTGGCACCTTCTCTCAACAGACCCTGTCTCAGCCAAAGTAGTAGTCTTGTCTGAGAAGTCACTGATCTCCAAGG
AAACAGATCTTACTGAGCCAACTCTGCTGGACGAACTAATCTGCCACATTGGTTCTTTGGCCTCTGTGTACCATAAGCCT
CCCAATGATTTTGTAGAAGGAAGTTATGGAATCCACTGCAAATACTTGCCAATTCATCATGGGAGCACTGATGCAGGTGA
CAGCCCTGTTGGCACCACCACTGCAACCAACCTGGAACAGCTCAGGTTATACCATCTCAAGGTGGCCTTCTAGGGGACCT
TTTGAACGTTGACCTTTGTCCCCTGGTCAGTGTGCCACAGGTATCATCCATACAGATGGGAGGAGTGGATCTCTTGGGAG
GAGGACTAGATAGTCTGGTTGGG

Alignment

ORF - retro_lafr_446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 62.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YLYLMNYAKSQPDMAIMAVNS-FVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVR
          YLYLMNY..SQPDMAIMAVN..FVKDCEDP.PLIRALAVRTMGCI.VDKITE.LCEPLRKCLKDED.Y..
Retrocopy YLYLMNYVRSQPDMAIMAVNC<FVKDCEDPHPLIRALAVRTMGCIWVDKITESLCEPLRKCLKDEDSYGQ

Parental  KTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHP-NSNLLDLNPQNINKL
          KTA.VC.AK.HDIN.QMVEDQGFLDSL.DLIADSNPMVVA.AVAALSEIS..HP.NSNLL..NPQNINKL
Retrocopy KTAVVCMAKFHDINTQMVEDQGFLDSL*DLIADSNPMVVASAVAALSEISKAHP<NSNLLNPNPQNINKL

Parental  LTALNECTEWGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYY
          LTALNECTE.GQIFILDCLSN.NPKD.R.AQ.ICE.VTP.LSHAN.AVVLSAVKVLMKFLELLPKDSDYY
Retrocopy LTALNECTE*GQIFILDCLSN*NPKDNRGAQTICEQVTPWLSHANAAVVLSAVKVLMKFLELLPKDSDYY

Parental  NMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLAS
          NMLLKKL.PPLV.LLSGE.EVQY.ALRNINLIVQ.R.EILKQEI.VF.VKYNDPIYVKLEKLDIMIRLAS
Retrocopy NMLLKKLDPPLVILLSGEAEVQYAALRNINLIVQERLEILKQEISVFLVKYNDPIYVKLEKLDIMIRLAS

Parental  QANIAQVLA-ELKEYATEVDVDFVRKAVRAI-GRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIR
          QAN.AQVL..ELKEYATEVDVDFVRKAV.A..G.CAIKVEQSAERCVSTLLDLIQTKVNYVVQEA.VVI.
Retrocopy QANTAQVLK<ELKEYATEVDVDFVRKAVQAM<GWCAIKVEQSAERCVSTLLDLIQTKVNYVVQEATVVIQ

Parental  DIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLL
          DIF.KYPNKYE..IATLCENLD.LDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDE.TQVQLTLL
Retrocopy DIFLKYPNKYEGTIATLCENLDWLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDETTQVQLTLL

Parental  TAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLI
          TAIVKLFLKK.SETQELVQQVLSLATQDS.NPDLRDRGYIYW.LLSTDPV.AK.VVLSEK.LIS.ETDL.
Retrocopy TAIVKLFLKKSSETQELVQQVLSLATQDSGNPDLRDRGYIYWHLLSTDPVSAKVVVLSEKSLISKETDLT

Parental  EPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQ-PQVIPSQ
          EPTLLDELICHIGSLASVYHKPPN.FVEGS.GIH.K.LPIHHGSTDAGDSPVGTTTATNLEQ..QVIPSQ
Retrocopy EPTLLDELICHIGSLASVYHKPPNDFVEGSYGIHCKYLPIHHGSTDAGDSPVGTTTATNLEQ<AQVIPSQ

Parental  GDLLGDLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG
          G.LLGDLLN.DL.P.V.VPQVSS.QMG.VDLLGGGLDSL.G
Retrocopy GGLLGDLLNVDLCPLVSVPQVSSIQMGGVDLLGGGLDSLVG

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_446 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Loxodonta africana	ENSLAFG00000015777	1 retrocopy	retro_lafr_446 ,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Mus musculus	ENSMUSG00000035152	1 retrocopy	retro_mmus_2503,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,
Pongo abelii	ENSPPYG00000008188	1 retrocopy	retro_pabe_3793,
Pan troglodytes	ENSPTRG00000009021	1 retrocopy	retro_ptro_3248,
Rattus norvegicus	ENSRNOG00000009988	2 retrocopies	retro_rnor_1267, retro_rnor_574,