RetrogeneDB ID: retro_mmus_200

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:92077056..92079213(+)
• Located in intron of: ENSMUSG00000039680

Retrocopy information

• Ensembl ID: ENSMUSG00000089774
• Aliases: Slc5a3, AA623876, BF642829, Smit1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Slc5a2
• Ensembl ID: ENSMUSG00000030781
• Aliases: Slc5a2, Sglt2
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 2 [Source:MGI Symbol;Acc:MGI:2181411]

Sequence

>retro_mmus_200
ATGAGGGCTGTACTGGAGGCAGCAGACATTGCCGTAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGCTTTTTTGC
CATGTGGAAATCTAATAGAAGCACTGTGAGTGGATACTTCCTGGCCGGGCGCTCTATGACCTGGGTGGCGATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAACACTTCATTGGGCTGGCAGGATCTGGAGCAGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTCTTGCAACTTCTGGGATGGGTTTTCATCCCCATTTACATCCGGTCAGGGGTATA
TACCATGCCTGAATACTTGTCCAAGAGGTTCGGTGGCCATAGGATTCAGGTCTATTTTGCAGCCTTGTCTCTGCTTCTCT
ATATCTTCACCAAGCTCTCAGTGGATCTGTATTCAGGGGCCCTCTTTATCCAGGAGTCCTTGGGTTGGAACCTTTATGTG
TCTGTCATCCTGCTCATTGGCATGACTGCTCTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCT
GCAGGCCCTGCTCATGATCATTGGGGCGCTCACACTTATGGTTATTAGCATGGTGAAGATTGGAGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCTGATGTTGCTTCCATTTTGTTGAAGTACAACCTTTCCAACACAAATGCTTGTATG
GTCCATCCTAAGGCGAATGCCCTAAAAATGTTGAGAGACCCAACAGATGAAGATGTTCCATGGCCTGGATTCATTCTTGG
GCAAACCCCAGCCTCGGTATGGTACTGGTGTGCTGACCAAGTCATCGTACAGAGGGTTCTAGCAGCCAAAAACATTGCTC
ATGCCAAAGGCTCCACTCTAATGGCTGGCTTCTTGAAGCTTCTACCAATGTTTATCATAGTTGTACCAGGAATGATTTCC
AGGATAGTGTTTGCTGATGAGATAGCTTGCATCAACCCAGAACACTGCATGCAAGTGTGTGGAAGCAGAGCTGGCTGCTC
CAATATTGCTTACCCACGCCTGGTGATGACCTTGGTTCCTGTGGGCCTTCGGGGCCTGATGATGGCAGTGATGATTGCAG
CTCTGATGAGTGACTTGGACTCCATCTTTAACAGCGCCAGTACCATATTCACCCTCGATGTGTACAAACTTATCCGCAAG
AGTGCAAGCTCCCGGGAACTAATGATTGTGGGCAGGATATTTGTGGCTTTTATGGTTGTCATCAGCATAGCATGGGTGCC
AATTATTGTGGAGATGCAAGGAGGCCAAATGTACCTTTACATCCAGGAGGTGGCAGATTATCTGACTCCTCCCGTGGCAG
CCCTCTTCCTTCTGGCAATTTTCTGGAAACGCTGCAATGAGCAAGGGGCTTTTTATGGTGGAATGGCAGGCTTTGTTCTT
GGAGCTGTCCGTTTGATACTGGCTTTTACCTACCGTGCTCCTGAGTGTGATCAACCTGATAACAGGCCAGGCTTCATCAA
AGACATCCATTATATGTACGTGGCTACGGCATTATTTTGGATCACAGGACTCATTACTGTGATTGTTAGTCTTCTCACAC
CACCTCCCACAAAGGATCAGATTCGTACCACTACCTTTTGGTCAAAGAAGACCCTGGTGACAAAGGAGAGCTGTTCTCAG
AAAGACGAACCATACAAAATGCAAGAGAAGAGCATCCTGCAGTGCAGCGAGAATAGCGAAGTCATCAGCCATACTATTCC
CAACGGGAAGTCTGAAGACAGCATTAAGGGACTGCAACCTGAAGACGTTAATCTGCTGGTGACATGCCGAGAAGAGGGCA
ACCCAGTGGCTTCCATGGGTCATTCAGAGGCAGAAACACCAGTAGATGCTTATTCCAATGGGCAAGCAGCTCTCATGGGT
GAGAGAGAAAGAGAGAAGGAAACGGAAAATAGAAGCCGGTATTGGAAGTTCATAGACTGGTTTTGTGGCTTTAAGAGTAA
AAGCCTTAGCAAGAGGAGCCTCAGAGACTTGATGGATGAGGAGGCTGTGTGTTTACAAATGTTAGAAGAGACTCCACAAG
TTAAAGTGATCCTAAACATTGGACTTTTTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTTTATTTCTCCTTATGA

Alignment

ORF - retro_mmus_200 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.76 %
• Parental protein coverage: 80.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADILVIAAYFLLVIGVGLWSMFRTNRGTVGGYFLAGRSMVWWPVGASLFASNIGSGHFVGLAGTGAASGL
          ADI.V.A.YF.LV...G...M...NR.TV.GYFLAGRSM.W...GASLF.SNIGS.HF.GLAG.GAASG.
Retrocopy ADIAVVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

Parental  AVAGFEWNALFVVLLLGWLFVPVYLTAGVITMPQYLRKRFGGHRIRLYLSVLSLFLYIFTKISVDMFSGA
          AV...E.NAL....LLGW.F.P.Y...GV.TMP.YL.KRFGGHRI..Y...LSL.LYIFTK.SVD..SGA
Retrocopy AVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLLLYIFTKLSVDLYSGA

Parental  VFIQQALGWNIYASVIALLGITMIYTVTGGLAALMYTDTVQTFVILAGAFILTGYAFHEVGGYSGLFDKY
          .FIQ..LGWN.Y.SVI.L.G.T...TVTGGL.A..YTDT.Q......GA..L........GG.......Y
Retrocopy LFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMVISMVKIGGFEEVKRRY

Parental  LGAMTSL-TVSKDPSVGNISSTCYQPRPDSYHLLRDPVTGDLPWPALLLGLTIVSGWYWCSDQVIVQRCL
          ..A..............N.......P.......LRDP...D.PWP...LG.T..S.WYWC.DQVIVQR.L
Retrocopy MLASPDVASILLKYNLSNTNACMVHPKANALKMLRDPTDEDVPWPGFILGQTPASVWYWCADQVIVQRVL

Parental  AGKNLTHIKAGCILCGYLKLMPMFLMVMPGMISRILYPDEVACVVPEVCKRVCGTEVGCSNIAYPRLVVK
          A.KN..H.K......G.LKL.PMF..V.PGMISRI...DE.AC..PE.C..VCG...GCSNIAYPRLV..
Retrocopy AAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRIVFADEIACINPEHCMQVCGSRAGCSNIAYPRLVMT

Parental  LMPNGLRGLMLAVMLAALMSSLASIFNSSSTLFTMDIYTRLRPRAGDKELLLVGRLWVVFIVAVSVAWLP
          L.P.GLRGLM.AVM.AALMS.L.SIFNS.ST.FT.D.Y...R..A...EL..VGR..V.F.V..S.AW.P
Retrocopy LVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVVISIAWVP

Parental  VVQAAQGGQLFDYIQSVSSYLAPPVSAVFVLALFVPRVNEKGAFWGLVGGLLMGLARLIPEFFFGSGSCV
          .....QGGQ...YIQ.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RLI..F......C.
Retrocopy IIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLILAFTYRAPECD

Parental  RPSACPALFCRVHYLYFAIILFICSGILTLGISLCTAPIPQKHLHRLVF
          .P...P......HY.Y.A..LF...G..T...SL.T.P..........F
Retrocopy QPDNRPGFIKDIHYMYVATALFWITGLITVIVSLLTPPPTKDQIRTTTF

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
SRP007412_brain	7.85 RPM	0.02 RPM
SRP007412_cerebellum	8.25 RPM	0.17 RPM
SRP007412_heart	2.21 RPM	0.19 RPM
SRP007412_kidney	57.34 RPM	411.11 RPM
SRP007412_liver	2.68 RPM	0.05 RPM
SRP007412_testis	3.16 RPM	1.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_200 was not detected

EST

2 EST(s) were mapped to retro_mmus_200 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BB814968	92078229	92078654	97.9	419	4	410
BB822301	92078286	92078751	96.4	458	6	445

TSS

No TSS is located nearby retro_mmus_200 retrocopy 5' end.

Lab

retro_mmus_200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_200 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_794

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 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	ENSMUSG00000006641	2 retrocopies	retro_mmus_2835, retro_mmus_2836,
Mus musculus	ENSMUSG00000030781	1 retrocopy	retro_mmus_200 ,
Pteropus vampyrus	ENSPVAG00000012531	1 retrocopy	retro_pvam_13,
Tursiops truncatus	ENSTTRG00000012500	1 retrocopy	retro_ttru_2,