RetrogeneDB ID: retro_btau_287

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:709957..711622(-)
• Located in intron of: ENSBTAG00000012594

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.62759
• Ensembl ID: ENSBTAG00000010096
• Aliases: None
• Description: sodium/glucose cotransporter 2 [Source:RefSeq peptide;Acc:NP_976236]

Sequence

>retro_btau_287
GCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGCCATGTGGAAATCTAATAGAAG
CACCGTGAGTGGATACTTCTTGGCGGGGCGCTCTATGACCTGGGTAGCAATTGGTGCCTCTCTATTTGTGAGCAATATTG
GGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCGGCAAGTGGATTTGCAGTGGGCGCATGGGAGTTCAATGCCTTG
CTGCTTTTGCAACTTCTGGGATGGGTTTTCATCCCGATTTACATCCGGTCAGGGGTATACACCATGCCTGAATACTTGTC
CAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTCGCAGCGTTGTCTCTGATTCTCTATATCTTCACCAAGCTCTCTG
TGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTCTATGTGTCTGTCATCCTGCTCATTGGC
ATGACCGCTTTGTTGACCGTCACCGGAGGCCTTGTCGCAGTAATCTACACAGACACCTTGCAGGCTCTGCTCATGATCGT
TGGGGCACTCACACTTATGGTGATTAGCATGATGGAGATTGGCGGGTTTGAGGAAGTTAAGAGAAGGTACATGTTGGCCT
CACCCAATGTCACTTCCATCCTGCTGACGTACAACCTTTCCAACACAAATTCTTGTAATGTCCACCCCAAGAAAGACGCA
CTGAAAATGTTGCGGAACCCAACAGATGAAGATGTTCCTTGGCCTGGATTCATCCTTGGGCAGACCCCGGCTTCAGTCTG
GTACTGGTGTGCCGACCAGGTCATCGTGCAGAGGGTCCTAGCAGCCAAAAACATTGCTCATGCCAAAGGCTCCACCCTGA
TGGCCGGCTTCCTGAAGCTTCTGCCAATGTTTATCATAGTGGTCCCCGGAATGATTTCCCGGATACTGTTTGCCGATGAC
ATAGCTTGCATCAACCCCGAGCACTGCATGCAGGTGTGTGGAAGCAGAGCTGGGTGCTCTAACATTGCCTACCCGCGCCT
CGTGATGAAGCTGGTTCCCGTGGGCCTCCGGGGCCTGATGATGGCCGTGATGATTGCCGCTCTGATGAGTGACTTGGACT
CCATCTTCAACAGCGCCAGCACCATATTCACCCTCGATGTGTACAAACTCATCCGCAAGAGCGCCAGTTCCCGGGAACTG
ATGATCGTGGGCAGGATATTTGTGGCCTTCATGGTGGTGATCAGCATCGCGTGGGTGCCCATCATCGTGGAGATGCAAGG
AGGCCAGATGTACCTTTACATCCAGGAGGTAGCTGACTACCTGACGCCCCCAGTTGCAGCCCTGTTCCTTCTGGCCATTT
TCTGGAAGCGCTGCAATGAACAAGGGGCTTTCTATGGTGGAATGGCGGGCTTTATCCTTGGAGCAGTCCGCTTGACACTG
GCCTTTGCCTACCGTGCCCCGGAATGTGACCAACCTGATAACAGGCCAGTCTTCATTAAAGACATCCATTACATGTATGT
GGCCACAGCGTTGTTTTGGATCACAGGACTCATTACTGTAATTGTTAGCCTTCTCACACCACCTCCTACGAAGGAACAGA
TTCGCACCACCACTTTTTGGTCTAAGAAGAGCCTGGTGGTCAAGGAGAGCTGCTCCCCGAAAGAT

Alignment

ORF - retro_btau_287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.71 %
• Parental protein coverage: 82.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADILVIAAYFLLVIGVGLWSMCRTNRGTVGGYFLAGRNMVWWPVGASLFASNIGSGHFVGLAGTGAASGL
          ADI...A.YF.LV...G...M...NR.TV.GYFLAGR.M.W...GASLF.SNIGS.HF.GLAG.GAASG.
Retrocopy ADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASGF

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

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

Parental  LRA---VTSLTVSEDPAVGNISSSCYRPRPDSYHLLRDPVTGDLPWPALLLGLTIVSSWYWCSDQVIVQR
          ..A...VTS..........N..S....P..D....LR.P...D.PWP...LG.T..S.WYWC.DQVIVQR
Retrocopy MLASPNVTSILLTYN--LSNTNSCNVHPKKDALKMLRNPTDEDVPWPGFILGQTPASVWYWCADQVIVQR

Parental  CLAGKNLTHIKAGCILCGYLKLMPMFLMVMPGMISRVLYPDEVACVVPEVCKRVCGTEVGCSNIAYPRLV
          .LA.KN..H.K......G.LKL.PMF..V.PGMISR.L..D..AC..PE.C..VCG...GCSNIAYPRLV
Retrocopy VLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIAYPRLV

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

Parental  LPVVQAAQGGQLFDYIQSVSSYLAPPVSAVFVLALFVPRVNEKGAFWGLIGGLLMGLARLVPEFSFGSGS
          .P.....QGGQ...YIQ.V..YL.PPV.A.F.LA.F..R.NE.GAF.G...G...G..RL...F......
Retrocopy VPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFILGAVRLTLAFAYRAPE

Parental  CVRPSGCPALLCRVHYLYFAILLFVCSGLLTLVVSLCTPPIPRKHLYRLVFSLRHSKEEREDLDAEE
          C..P...P......HY.Y.A..LF...GL.T..VSL.TPP..........F....S....E......
Retrocopy CDQPDNRPVFIKDIHYMYVATALFWITGLITVIVSLLTPPPTKEQIRTTTFWSKKSLVVKESCSPKD

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
ERP005899_liver	0.29 RPM	1.95 RPM
ERP005899_muscle	6.23 RPM	8.13 RPM
SRP017611_brain	11.69 RPM	4.61 RPM
SRP017611_kidney	24.42 RPM	280.12 RPM
SRP017611_liver	0.45 RPM	14.42 RPM
SRP030211_testis	1.24 RPM	11.09 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_287 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_287 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_105
Oryctolagus cuniculus	retro_ocun_1633

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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,