RetrogeneDB ID: retro_lcha_35

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126701.1:661121..662780(+)
• Located in intron of: ENSLACG00000011712

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSLACG00000007334
• Aliases: None
• Description: None

Sequence

>retro_lcha_35
GACATTGCCATAGTAGCACTGTATTTTGTGCTTGTATTAACCATTGGCTTTTTTGCCATGTGGAAATCGAACAGAAGTAC
TGTAAGCGGGTATTTTTTGGCTGGGCGTTCCATGACTTGGGCTGCAGTTGGTGCTTCTTTATTTGTGAGTAATATCGGCA
GTGAACATTTCATCGGGCTTGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTAGGGGCTTGGGAGTTGAATGCTGTACTG
CTTTTGCAACTTCTAGGATGGGTGTTTATCCCAGTCTACATAAGGTCAGGAGTCTACACTATGCCAGAATACCTGTCTAA
ACGTTATGGAGGTCACAGGATTCAGATATATTTTGCTGGTCTGTCTTTGCTTCTCTATGTCTTTACAAAGCTCTCTGTGG
ACCTTTATGCTGGGGCTCTGTTTATTCAAGAATCACTGGGTTGGAACCTGTACCTCTCTGTTATCTTACTGATTGGGATG
ACTGCTCTGTTAACAGTTACTGGAGGACTTGTAGCAGTTATTTACACAGATACCCTTCAAGCCATTCTCATGGTTGTTGG
TGCCCTCATCCTCATGGTTGCTGGCATTGTAGAGGTTGGGGGTTTTGAAGAACTCAAGCGGAGATATATGCTAGCCACAC
CAAATGTCACAGGAATCCTGTTGAGCCACAACTTTACCAACAATTTTGTTTGCCATGTGGATCCAAAGCCAGACTCCCTG
AAGATGCTACGTGAGCCTTCAGATGAAGATATCCCCTGGCCTGGTTTCCTGCTAGGGCAGACTCCAGCTTCAGTTTGGTA
TTGGTGTGCTGATCAAGTCATAGTCCAGAGAGTGCTAGCAGCAAAGAACATTGCTCATGCTAAAGGATCCACTCTAATGG
CTGGCTTCCTCAAACTCTTACCATTGTTCATTATAGTTGTGCCAGGAATGATTTCAAGAGTACTTTTTGTAGATGATATT
GTATGTATTAACCCTGAGCATTGCATGGAAGTCTGTGGAAGCAAAGCTGGATGCTCCAATATAGCTTATCCACGTCTGGT
AATGAAAATCCTTCCAGTTGGTTTAAGGGGACTTATGATGGCTGTGATGATTGCTGCCTTGATGAGTGATCTGGATTCCA
TATTTAACAGTGCCAGCACAATATTTACTCTTGACATCTACAAGTATTTTCGAAAGGCAGCTACCTCTCGAGAAATGGTG
ATTGTGGGCAGAGTTTTTGTTGTGTTCATGGTGGTTGTAAGCATTGCTTGGGTTCCAATAATTGTTGAAATGCAGGGAGG
CCAAATGTACCTGTATATCCAAGAAGTGGCAGATTATTTGACTCCACCAGTGGCTGCTCTCTTCATTCTGGGCGTTATCT
GGAAGCGCTGCAACGAGTTTGGAGCATTCTATGGTGGAATGGTTGGCTTTGTTTTAGGAGTCACTCGTTTGATTCTGGCT
TTTGTCTACCGAGTCCCAGAATGCAATCAGCCTGACACAAGGCCAAGTTTTATCAGAAATGTACACTACATGTACATAGC
TACAACTTTGTTCTGGATCACTGTGGCTGTCACAGTTATAGTTAGTCTTCTGACTCCACCCCCTACAAAAGAACAGATTC
GTACCACCACCATCTGGTCCCTGAAAGACAGAAATATTGAGCAAACCAGTTTTGAGGAA

Alignment

ORF - retro_lcha_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.45 %
• Parental protein coverage: 80.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DICVIVAYFLLVIAVGLWSMCRMNRSTIGGYFLAGRSMVWGPIGASLFASNIGSGHFVGLAGTGAARGIA
          DI.....YF.LV...G...M...NRST..GYFLAGRSM.W...GASLF.SNIGS.HF.GLAG.GAA.G.A
Retrocopy DIAIVALYFVLVLTIGFFAMWKSNRSTVSGYFLAGRSMTWAAVGASLFVSNIGSEHFIGLAGSGAASGFA

Parental  VGGFEWIALLMVLLLGWLFVPVYLTAGVITMPQYLKKRFGGSRIGLYLTVLSLLIYIFTKISVDMFSGAI
          VG..E..A.L...LLGW.F.PVY...GV.TMP.YL.KR.GG.RI..Y...LSLL.Y.FTK.SVD...GA.
Retrocopy VGAWELNAVLLLQLLGWVFIPVYIRSGVYTMPEYLSKRYGGHRIQIYFAGLSLLLYVFTKLSVDLYAGAL

Parental  FIQQALGWNIYMAVIALLMITALYTVTGGLAALMYTDTFQTFIIIAGSFVLMGFAFYNVGGYGALFEKYQ
          FIQ..LGWN.Y..VI.L...TAL.TVTGGL.A..YTDT.Q......G...LM......VGG...L...Y.
Retrocopy FIQESLGWNLYLSVILLIGMTALLTVTGGLVAVIYTDTLQAILMVVGALILMVAGIVEVGGFEELKRRYM

Parental  NAVPVLHKSQDVARYNISMACFV-PRPDSYHLLRDPLSGDLPWPALIFGLTIISCWYWCTDQVIVQRCLA
          .A.P................C.V.P.PDS...LR.P...D.PWP....G.T..S.WYWC.DQVIVQR.LA
Retrocopy LATPNVTGILLSHNFTNNFVCHVDPKPDSLKMLREPSDEDIPWPGFLLGQTPASVWYWCADQVIVQRVLA

Parental  AKNLTHVKAGCIMCGYLKLLPMFLMVMPGMISRILYTDDVACVVPEECQRICGTEVGCSNIAYPKLVVTL
          AKN..H.K....M.G.LKLLP.F..V.PGMISR.L..DD..C..PE.C...CG...GCSNIAYP.LV...
Retrocopy AKNIAHAKGSTLMAGFLKLLPLFIIVVPGMISRVLFVDDIVCINPEHCMEVCGSKAGCSNIAYPRLVMKI

Parental  MPTGLRGLMLAVMLAALMSSLASIFNSSSTLFTMDIWTRLRPHAGDKELMIVGRVWILCIIAVSIAWIPV
          .P.GLRGLM.AVM.AALMS.L.SIFNS.ST.FT.DI....R..A...E..IVGRV.......VSIAW.P.
Retrocopy LPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDIYKYFRKAATSREMVIVGRVFVVFMVVVSIAWVPI

Parental  VQVAQSGQLFDYIQSITSYLAPPITAVFLLAVFVKRVNEPGAFWGLLGGLMVGLARMISEFVYGSGSCIF
          ....Q.GQ...YIQ....YL.PP..A.F.L.V..KR.NE.GAF.G...G...G..R.I..FVY....C..
Retrocopy IVEMQGGQMYLYIQEVADYLTPPVAALFILGVIWKRCNEFGAFYGGMVGFVLGVTRLILAFVYRVPECNQ

Parental  PSNCPWIICGIHYLYFAIILFLITCLLILGASLCTPAIPDKHLHRLVFSLRHSKEERIDLDSMQE
          P...P..I...HY.Y.A..LF.IT.......SL.TP..P.K...R........K...I...S..E
Retrocopy PDTRPSFIRNVHYMYIATTLFWITVAVTVIVSLLTPP-PTKEQIRTT-TIWSLKDRNIEQTSFEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	0.64 RPM	0.99 RPM
DRP000627_kidney	0.51 RPM	0.59 RPM
DRP000627_pectoral_fin	1.86 RPM	0.16 RPM
DRP000627_pelvic_fin	1.91 RPM	0.08 RPM
DRP000627_pharynx	0.14 RPM	1.43 RPM
DRP000627_tail_muscle	0.21 RPM	0.94 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_35 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae 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,