RetrogeneDB ID: retro_cfam_157

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 31:28632855..28635012(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000009546
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A2
• Ensembl ID: ENSCAFG00000016909
• Aliases: SLC5A2, SGLT2
• Description: Canis lupus familiaris solute carrier family 5 (sodium/glucose cotransporter), member 2 (SLC5A2), mRNA. [Source:RefSeq mRNA;Acc:NM_001007142]

Sequence

>retro_cfam_157
ATGAGGGCTGTACTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCAATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTCTGGGATGGGTTTTCATCCCGATTTACATCCGGTCAGGGGTATA
CACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTTGCAGCCTTGTCTCTGATTCTCT
ATATCTTCACCAAGCTCTCAGTGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTCTATGTG
TCTGTCATCCTGCTCATTGGCATGACTGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCT
ACAGGCTCTGCTTATGATCGTTGGGGCACTCACACTTATGATAATTAGCATGATGGAGATTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCAATGTTACTTCCATCTTGTTGACATACAACCTTTCCAACACAAATTCTTGTAAT
GTCCACCCTAAGAAAGATGCACTGAAAATGTTGCGGAATCCAACAGATGAAGATGTTCCTTGGCCTGGATTTGTTCTTGG
GCAGACCCCAGCTTCAGTATGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGAGTCTTAGCAGCTAAAAACATTGCTC
ATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTGAAGCTGCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGAATACTGTTTGCTGATGATATAGCTTGCATCAACCCAGAGCACTGCATGCAAGTATGTGGAAGCAGAGCTGGGTGCTC
TAATATTGCTTACCCACGCCTGGTGATGAAGCTGGTTCCTGTGGGCCTCCGTGGCTTAATGATGGCGGTGATGATTGCAG
CTCTGATGAGCGACTTGGACTCTATCTTTAACAGTGCCAGTACCATATTTACCCTTGACGTGTACAAACTCATCCGCCGG
AGCGCGAGCTCCCGGGAACTAATGATTGTGGGGAGGATATTTGTGGCTTTTATGGTGGTGATCAGCATTGCATGGGTGCC
AATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTACATTCAGGAGGTAGCTGATTACCTGACACCCCCAGTTGCGG
CCCTTTTCCTTCTGGCAATTTTCTGGAAGCGCTGTAATGAGCAAGGGGCTTTCTATGGTGGAATGGCTGGCTTTGTTCTT
GGAGCAGTCCGTTTGACACTGGCCTTTGCATACCGTGCCCCAGAATGTGACCAACCTGATAACAGGCCAGGCTTCATCAA
AGACATCCATTACATGTATGTGGCCACAGCATTGTTTTGGGTCACAGGACTCATTACAGTAATTGTTAGCCTTCTGACAC
CACCTCCCACAAAGGAACAGATTCGTACCACCACCTTTTGGTCTAAGAAGAGCCTGGTGGTGAAGGAAAGCTGCTCCCCG
AAAGATGAACCCTACAAAATGCAAGAGAAGAGCATTCTGAGGTGCAGTGAGAACAGTGAGGCCACCAACCACATCATTCC
CAATGGGAAGTCGGAAGATAGCATCAAGGGCCTTCAGCCAGAAGATGTTAATCTGTTGGTGACCTGCAGAGAAGAGGGCA
ATCCAGTGGCTTCGTTAGGGCATTCAGAGGCAGAAACACCAGTAGATGCTTATTCCAATGGGCAAGCAGCTCTTATGGGT
GAGAAAGAGAGAAAGAAGGAAACAGAGGATGGAGGCCGGTACTGGAAGTTCATAGATTGGTTCTGTGGCTTTAAAAGTAA
GAGCCTCAGCAAGAGGAGTCTCAGAGACCTGATGGAGGAGGAGGCTGTTTGTTTACAAATGTTGGAAGAGCCTCCACAAG
TTAAACTAATACTAAATATCGGACTTTTTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTTTATTTCTCCTTATGA

Alignment

ORF - retro_cfam_157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.36 %
• Parental protein coverage: 81.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SADILVIAAYFLLVIGVGLWSMCRTNRGTVGGYFLAGRSMVWWPVGASLFASNIGSGHFVGLAGTGAASG
          .ADI...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  AVFIQQALGWNIYASVIALLGITMIYTVTGGLAALMYTDTVQTFVILGGAFILMGYAFHEVGGYSGLFDK
          A.FIQ..LGWN.Y.SVI.L.G.T...TVTGGL.A..YTDT.Q......GA..LM.....E.GG.......
Retrocopy ALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMIISMMEIGGFEEVKRR

Parental  YLGAMTSL-TVSEDPAVGNISSSCYRPRPDSYHLLRDPVTGDLPWPALLLGLTIVSGWYWCSDQVIVQRC
          Y..A..............N..S....P..D....LR.P...D.PWP...LG.T..S.WYWC.DQVIVQR.
Retrocopy YMLASPNVTSILLTYNLSNTNSCNVHPKKDALKMLRNPTDEDVPWPGFVLGQTPASVWYWCADQVIVQRV

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

Parental  KLMPNGLRGLMLAVMLAALMSSLASIFNSSSTLFTMDIYTRLRPCAGDRELLLVGRLWVVFIVAVSVAWL
          KL.P.GLRGLM.AVM.AALMS.L.SIFNS.ST.FT.D.Y...R..A..REL..VGR..V.F.V..S.AW.
Retrocopy KLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRRSASSRELMIVGRIFVAFMVVISIAWV

Parental  PIVQAAQGGQLFDYIQAVSSYLAPPVSAVFVLALFVPRVNEKGAFWGLIGGLLMGLARLIPEFSYGSGSC
          PI....QGGQ...YIQ.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RL...F.Y....C
Retrocopy PIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLTLAFAYRAPEC

Parental  VQPSVCPALLCGMHYLYFAIVLFVCSGLLTLVISLCTAPIPRKHLHRLVFSLRHSKEERE
          .QP...P......HY.Y.A..LF...GL.T...SL.T.P..........F....S....E
Retrocopy DQPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPPPTKEQIRTTTFWSKKSLVVKE

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
SRP012049_cerebellum	0.00 RPM	10.92 RPM
SRP017611_brain	0.00 RPM	7.54 RPM
SRP017611_kidney	0.07 RPM	340.95 RPM
SRP017611_liver	0.00 RPM	7.18 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_157 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_157 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_157 has 0 orthologous retrocopies within eutheria group .

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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,