RetrogeneDB ID: retro_lafr_787

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_38:16103084..16104101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSLAFG00000003482
• Aliases: None
• Description: None

Sequence

>retro_lafr_787
TTTTTACCTACACCAACCCAGGTGTATCAGGACCAGCTTGAAGCCAAAGAAAAGGCAAATTCCCAGAGATCACAGCAAAA
CTCACTGGTGTCCTTTAGAAGAGGGCCTCCTCCATACAGGTGCCAGAAAGGCTGGAGACCTCTGCCCTTAGAGGATTTTG
GAGATGGAAGCACTTTTCCAGAAAACCATGTGGCCCAGTATCCACTGGATATGGGACAAAGGAAAATGGTGTTCAGTGAA
CTGATCGTTCAGGTGGATGATTAAGGAAAATTAAACTGGATCCAATTGTTCAATAAGGAAAAGTCAAAAGACAAGGTCAT
TTATAGCAAATACACTGACCTGATTCCCAAAGAAGTGGTGAATGCAGAAGACCCAGACCTGCAACGACCTAAGGAAGAAA
CCATTGAGATAAGAGAAAAGAATAGCCTTAGAAAAATCTGTATCAAGAAGGTCACCCAGGCCATGCCAGTTTGAGCAGCT
GATAAACTGGCTTCTGCTCTGTACATTCTGTAGACACTATCTCAGCAAGGAGTGACTTTCCACTCAGGAGCTAACTAGAG
GGTTATTTACATGGTAGAAATGCAAAAAGATCCAGTGGAACATCCAAGGTTAAAGATAAATAGGAAAACTCCTCCAGGAC
TACCTTTTCCTCCTGCAACTGTCATGCATTCTCCAAGTTAAAAGGTGGCCATGAAAGAACAAGACTGGGAGATTCTTCCT
TGTATATCAGAATGGAAAAACACAAAGAGTTGCACAATTCCATCAGACAAATGTCTGGCTCCTGAAGGATGAGGATTACA
GAGAGTTCATATCAATGAAAATTTAGCCAAACTAGCTGGTGCCCTCTGCATCGCTGATCACAAGGCTCATGAAGCTGTAG
AAATGCATGCCCAAGTAGAGAGAAAGATAGCTCAGAAAGAAAAGGAAAAATATGAATAGAAACTTTGAGAAACAGCTCAG
AAAGCCAGGGAGAGGAGAGCTGAGATCAAAGTCCATATGGAAAAAGACGATGGGAAG

Alignment

ORF - retro_lafr_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 63.99 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVAQYPLE
          FLP.PTQ..QDQLEA.EKA.SQRS.Q.SLVS.RR.PPPY...KGW.P..LEDFGDG..FPE.HVAQYPL.
Retrocopy FLPTPTQVYQDQLEAKEKANSQRSQQNSLVSFRRGPPPYRCQKGWRPLPLEDFGDGSTFPENHVAQYPLD

Parental  MGRKKKMSNALAIQVDAEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAIKEITE
          MG..K.....L..QVD..GK...........SKDKVIYSKYTDL.PKEV.NA.DPDLQRP.EE.I.EI.E
Retrocopy MGQRKMVFSELIVQVDD*GKLNWIQLFNKEKSKDKVIYSKYTDLIPKEVVNAEDPDLQRPKEETI-EIRE

Parental  KTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPPRFKIN
          K....L.K....KV..AMPV.AADKLA.A.YI..T.SQQGV.F.SGA..RVI.MVEMQKDP.E.PR.KIN
Retrocopy KN--SLRKICIKKVTQAMPV*AADKLASALYIL*TLSQQGVTFHSGAN*RVIYMVEMQKDPVEHPRLKIN

Parental  KKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHINENFA
          .K.P.G.P.PPA.VMHSPS.K...KE.Q.W.I.PCIS.WKN.K..TIP.DK.LA..G.GLQ.VHINEN.A
Retrocopy RKTPPGLPFPPATVMHSPS*KVAMKE-QDWEILPCISEWKNTKSCTIPSDKCLAPEG*GLQRVHINENLA

Parental  KLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGE
          KLA.AL.IAD.KA.EAVEM.AQVERK.AQKEKEK.E.KL.E.AQKARERRA.IK.H.EK.DG.
Retrocopy KLAGALCIADHKAHEAVEMHAQVERKIAQKEKEKYE*KL*ETAQKARERRAEIKVHMEKDDGK

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_787 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 21 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781, retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787 ,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,