RetrogeneDB ID: retro_lafr_54

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_13:21899474..21901631(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000017379
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSLAFG00000005737
• Aliases: None
• Description: None

Sequence

>retro_lafr_54
ATGAGGGCTGTACTGGAGACGGCAGACATTGCCATAGTGGCCCTGTACTTTATCCTGGTCATGTGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCAATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAACACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTTTGGGATGGGTTTTCATCCCGATTTACATCCGGTCAGGGGTATA
CACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTCAGGTGTATTTCGCAGCCTTGTCTCTGATCCTCT
ATATCTTCACCAAGCTCTCAGTGGATTTGTATTCAGGTGCCCTCTTTATCCAAGAGTCTTTGGGTTGGAACCTTTATGTA
TCTGTCATCCTGCTCATTGGTATGACTGCCTTGCTGACTGTCACCGGAGGCCTTGTTGCGGTGATCTACACAGACACTCT
GCAGGCTTTGCTCATGATCATTGGGGCACTGACTCTCATGGTTATTAGCATGATGGAGATTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCGCCCAATGTCACTTCCATCTTGTTAACGTACAACTTGTCCAACACAAATTCTTGTAAT
GTCCACCCTAAGAAAGATGCCCTGAAAATGTTGCGGAATCCAACAGATGAAGATGTCCCTTGGCCTGGATTCATTCTTGG
GCAGACCCCAGCTTCGGTGTGGTACTGGTGCGCTGACCAAGTCATCGTGCAGAGGGTCTTAGCAGCCAAAAACATCGCCC
ATGCCAAAGGCTCTACTCTGATGGCTGGATTCTTGAAGCTTCTGCCAATGTTTATCATAGTGGTCCCAGGAATGATTTCC
AGGATACTGTTTGCTGATGACATAGCTTGCATCAACCCAGAGCACTGCATGCAGGTGTGTGGAAGCAGAGCCGGCTGCTC
CAATATTGCCTACCCACGCCTGGTGATGAAGCTGGTTCCTGTGGGGCTTCGGGGCCTGATGATGGCGGTGATGATTGCAG
CTCTGATGAGTGACTTGGACTCCATCTTTAACAGTGCCAGCACCATATTTACCCTCGATGTGTACAAACTCATCCGCAAG
AGCGCAAGCTCTCGGGAACTGATGATTGTGGGGAGGATATTTGTGGCTTTTATGGTGGTGATTAGCATTGCCTGGGTGCC
AATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTACATTCAAGAGGTAGCAGATTACCTGACACCTCCGGTTGCGG
CCCTCTTCCTCCTGGCAATTTTCTGGAAGCGTTGCAATGAGCAAGGGGCTTTCTATGGTGGGATGGCAGGCTTTGTTCTT
GGAGCAATCCGTTTGACGCTGGCCTTTACCTACCGTGCCCCAGAGTGTGACCAGCCTGATAACAGACCAGGCTTCATCAA
AGACATCCATTACATGTATGTGGCCACAGCATTGTTTTGGGTCACAGGACTCATTACTGTAATTGTTAGCCTTCTCACAC
CACCTCCCACGAAGGAACAGATTCGTACCACCACCTTTTGGTCTAAGAGGAGCGTGGTGGTGAAGGAGAGCTGTTCCCCG
AAGGATGAACCATACAAGATGCAAGAGAAAAGCATTCTGAGGTGCAGTGAGAACAGCGAGGCCATCAACCACGTCATTCC
CAATGGGAAATCTGAAGACAGCATTAAGGGCCTTCAGCCTGAAGACGTGAATCTGTTGGTGACCTGCAGAGAGGAAGGCA
ACCCAGTGGCTTCCTTAGGTCACTCTGAGGCAGAAACACCAGTGGATGCTTATTCCAACGGGCAGGCAGCTCTCATGGGT
GAGAAAGAGAGAAAGAAAGAAATGGAGGATGGCAGCCGGTACTGGAATTTCATAGACTGGTTCTGTGGCTTTAAAAGTAA
GAGCCTCAGCAAGAGGAGTCTCAGAGACCTGATGGAGGAGGAGGCTGTTTGTTTACAAATGTTGGAAGAGACTCCAAAAG
TTAAAGTAATACTGAATATTGGACTTTTTGCTGTGTGTTCTCTTGGAATTTTCATGTTCGTTTATTTCTCCTTATGA

Alignment

ORF - retro_lafr_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.84 %
• Parental protein coverage: 80.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLDILVIAAYFLLVIGVGLWSMCRTNRGTVGGYFLAGRSMLWWPVGASLFASNIGSGHFVGLAGTGAASG
          T.DI...A.YF.LV...G...M...NR.TV.GYFLAGRSM.W...GASLF.SNIGS.HF.GLAG.GAASG
Retrocopy TADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASG

Parental  LAVAGFEWNALFVVLLLGWLFAPVYLTAGVITMPQYLRKRFGGHRIRLYLSVLSLFLYIFTKISVDMFSG
          .AV...E.NAL....LLGW.F.P.Y...GV.TMP.YL.KRFGGHRI..Y...LSL.LYIFTK.SVD..SG
Retrocopy FAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSG

Parental  AVFIQQALGWNIYASVIALLGITMVYTVTGGLAALMYTDTVQTFVILGGAFILMGYAFHEVGGYSGLFDK
          A.FIQ..LGWN.Y.SVI.L.G.T...TVTGGL.A..YTDT.Q......GA..LM.....E.GG.......
Retrocopy ALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMVISMMEIGGFEEVKRR

Parental  YLGAVPSL-TVSEDPALGNISSSCYRPRPDSYHLLRDPVTGDLPWPALLLGLTIVSGWYWCSDQVIVQRC
          Y..A.P..........L.N..S....P..D....LR.P...D.PWP...LG.T..S.WYWC.DQVIVQR.
Retrocopy YMLASPNVTSILLTYNLSNTNSCNVHPKKDALKMLRNPTDEDVPWPGFILGQTPASVWYWCADQVIVQRV

Parental  LAGKNLTHIKAGCILCGYLKLMPMFLMVMPGMISRILYPDEVACVVPEVCKRVCGTEVGCSNIAYPRLVV
          LA.KN..H.K......G.LKL.PMF..V.PGMISRIL..D..AC..PE.C..VCG...GCSNIAYPRLV.
Retrocopy LAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIAYPRLVM

Parental  KLMPNGMRGLMLAVMLAALMSSLASIFNSSSTLFTMDIYTRLRPCASDRELLLVGRLWVVFIVAVSVAWL
          KL.P.G.RGLM.AVM.AALMS.L.SIFNS.ST.FT.D.Y...R..AS.REL..VGR..V.F.V..S.AW.
Retrocopy KLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVVISIAWV

Parental  PVVQAAQGGQLFDYIQAVSSYLAPPVSAVFMLALFVPRVNEKGAFWGLIGGLLMGLARLIPEFSFGSGSC
          P.....QGGQ...YIQ.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RL...F......C
Retrocopy PIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAIRLTLAFTYRAPEC

Parental  VRPSKCPALLCGVHYLYFAIVLFVCSGLLTLIVSLCTAPIPRKHLHRLVFSLRHS
          ..P...P......HY.Y.A..LF...GL.T.IVSL.T.P..........F....S
Retrocopy DQPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPPPTKEQIRTTTFWSKRS

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_54 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011926	1 retrocopy	retro_acar_109,
Ailuropoda melanoleuca	ENSAMEG00000016218	1 retrocopy	retro_amel_32,
Bos taurus	ENSBTAG00000010096	1 retrocopy	retro_btau_287,
Canis familiaris	ENSCAFG00000016909	1 retrocopy	retro_cfam_157,
Felis catus	ENSFCAG00000001380	1 retrocopy	retro_fcat_110,
Latimeria chalumnae	ENSLACG00000007334	1 retrocopy	retro_lcha_35,
Loxodonta africana	ENSLAFG00000005737	1 retrocopy	retro_lafr_54 ,
Myotis lucifugus	ENSMLUG00000011500	1 retrocopy	retro_mluc_218,
Mus musculus	ENSMUSG00000030781	1 retrocopy	retro_mmus_200,
Pteropus vampyrus	ENSPVAG00000012531	1 retrocopy	retro_pvam_13,
Tursiops truncatus	ENSTTRG00000012500	1 retrocopy	retro_ttru_2,