RetrogeneDB ID: retro_hsap_105

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:35467497..35469654(+)
• Located in intron of: ENSG00000214955

Retrocopy information

• Ensembl ID: ENSG00000198743
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSG00000100170
• Aliases: SLC5A1, D22S675, NAGT, SGLT1
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 [Source:HGNC Symbol;Acc:11036]

Sequence

>retro_hsap_105
ATGAGAGCTGTACTGGACACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAACAATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTACAACTTCTGGGATGGGTTTTCATCCCAATTTACATCCGGTCAGGGGTATA
TACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTTGCAGCCTTGTCTCTGATTCTCT
ATATTTTCACCAAGCTCTCGGTGGATCTGTATTCGGGTGCCCTTTTTATCCAGGAGTCTTTGGGTTGGAATCTTTATGTG
TCTGTCATCCTGCTCATTGGCATGACTGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCT
GCAGGCTCTGCTCATGATCATTGGGGCACTTACACTTATGATTATTAGCATAATGGAGATTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCGATGTCACTTCCATCTTATTGACATACAACCTTTCCAACACAAATTCTTGTAAT
GTCTCCCCTAAGAAAGAAGCCCTGAAAATGCTGCGGAATCCAACAGATGAAGATGTTCCTTGGCCTGGATTCATTCTTGG
GCAGACCCCAGCTTCAGTATGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTCCTTGCAGCCAAAAACATTGCTC
ATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTAAAGCTCCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGGATACTGTTTACTGATGATATAGCTTGCATCAACCCAGAGCACTGCATGCTGGTGTGTGGAAGCAGAGCTGGTTGCTC
CAATATTGCTTACCCACGCCTGGTGATGAAGCTGGTTCCTGTGGGCCTTCGGGGTTTAATGATGGCAGTGATGATTGCAG
CTCTGATGAGTGACTTAGACTCTATCTTTAACAGTGCCAGTACCATATTCACCCTCGATGTGTACAAACTTATCCGCAAG
AGCGCAAGCTCCCGGGAGTTAATGATTGTGGGGAGGATATTTGTGGCATTTATGGTGGTGATCAGCATAGCATGGGTGCC
AATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTACATTCAGGAGGTAGCAGATTACCTGACACCCCCAGTGGCAG
CCTTGTTCCTGCTGGCAATTTTCTGGAAGCGCTGCAATGAACAAGGGGCTTTCTATGGTGGAATGGCTGGCTTTGTTCTT
GGAGCAGTCCGTTTGATACTGGCCTTTGCCTACCGTGCCCCAGAATGTGACCAACCTGATAATAGGCCGGGCTTCATCAA
AGACATCCATTATATGTATGTGGCCACAGGATTGTTTTGGGTCACGGGACTCATTACTGTAATTGTGAGCCTTCTCACAC
CACCTCCCACAAAGGAACAGATTCGAACCACCACCTTTTGGTCTAAGAAGAACCTGGTGGTGAAGGAGAACTGCTCCCCA
AAAGAGGAACCATACCAAATGCAAGAAAAGAGCATTCTGAGATGCAGTGAGAATAATGAGACCATCAACCACATCATTCC
CAACGGGAAATCTGAAGACAGCATTAAGGGCCTTCAGCCTGAAGATGTTAATCTGTTGGTAACCTGCAGAGAGGAGGGCA
ACCCAGTGGCATCCTTAGGTCATTCAGAGGCAGAAACACCAGTTGACGCTTACTCCAATGGGCAAGCAGCTCTCATGGGT
GAGAAAGAGAGAAAGAAAGAAACGGATGATGGAGGTCGGTACTGGAAGTTCATAGACTGGTTTTGTGGCTTTAAAAGTAA
GAGCCTCAGCAAGAGGAGTCTCAGAGACCTGATGGAAGAGGAGGCTGTTTGTTTACAGATGCTAGAAGAGACTCGGCAAG
TTAAAGTAATACTAAATATTGGACTTTTTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTTTATTTCTCCTTATGA

Alignment

ORF - retro_hsap_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.08 %
• Parental protein coverage: 79.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRNAADISIIVIYFVVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGLAGTGA
          ....ADI.I...YF..VM..G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SNIGS.HF.GLAG.GA
Retrocopy VLDTADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVTIGASLFVSNIGSEHFIGLAGSGA

Parental  ASGIAIGGFEWNALVLVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGQRIQVYLSLLSLLLYIFTKISADI
          ASG.A.G..E.NAL.L...LGW.F.PIYI..GV.TMPEYL.KRFGG.RIQVY...LSL.LYIFTK.S.D.
Retrocopy ASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDL

Parental  FSGAIFINLALGLNLYLAIFLLLAITALYTITGGLAAVIYTDTLQTVIMLVGSLILTGFAFHEVGGYDAF
          .SGA.FI...LG.NLY....LL...TAL.T.TGGL.AVIYTDTLQ...M..G.L.L......E.GG....
Retrocopy YSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMIISIMEIGGFEEV

Parental  MEKYMKAIP---TIVSDGNTTFQEKC-YTPRADSFHIFRDPLTGDLPWPGFIFGMSILTLWYWCTDQVIV
          ...YM.A.P....I....N......C...P........R.P...D.PWPGFI.G......WYWC.DQVIV
Retrocopy KRRYMLASPDVTSILLTYNLSNTNSCNVSPKKEALKMLRNPTDEDVPWPGFILGQTPASVWYWCADQVIV

Parental  QRCLSAKNMSHVKGGCILCGYLKLMPMFIMVMPGMISRILYTEKIACVVPSECEKYCGTKVGCTNIAYPT
          QR.L.AKN..H.KG.....G.LKL.PMFI.V.PGMISRIL.T..IAC..P..C...CG...GC.NIAYP.
Retrocopy QRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFTDDIACINPEHCMLVCGSRAGCSNIAYPR

Parental  LVVELMPNGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYAKVRKRASEKELMIAGRLFILVLIGISI
          LV..L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y...RK.AS..ELMI.GR.F......ISI
Retrocopy LVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVVISI

Parental  AWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLILGLLIGISRMITEFAYGT
          AWVPI....Q.GQ...YIQ....YL.PP.AA.FLLAIFWKR.NE.GAF.G...G...G..R.I..FAY..
Retrocopy AWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLILAFAYRA

Parental  GSCMEPSNCPTIICGVHYLYFAIILFAISFITIVVISLLTKP
          ..C..P.N.P..I...HY.Y.A..LF.......V..SLLT.P
Retrocopy PECDQPDNRPGFIKDIHYMYVATGLFWVTGLITVIVSLLTPP

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
bodymap2_adipose	14.09 RPM	0.12 RPM
bodymap2_adrenal	2.31 RPM	0.00 RPM
bodymap2_brain	4.15 RPM	0.26 RPM
bodymap2_breast	7.24 RPM	12.72 RPM
bodymap2_colon	9.65 RPM	2.05 RPM
bodymap2_heart	1.31 RPM	313.04 RPM
bodymap2_kidney	22.81 RPM	4.41 RPM
bodymap2_liver	1.50 RPM	6.32 RPM
bodymap2_lung	3.46 RPM	2.97 RPM
bodymap2_lymph_node	17.27 RPM	0.04 RPM
bodymap2_ovary	5.42 RPM	1.27 RPM
bodymap2_prostate	2.70 RPM	2.44 RPM
bodymap2_skeletal_muscle	1.18 RPM	0.00 RPM
bodymap2_testis	7.96 RPM	6.45 RPM
bodymap2_thyroid	42.35 RPM	0.70 RPM
bodymap2_white_blood_cells	6.91 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_105 was not detected

EST

8 EST(s) were mapped to retro_hsap_105 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE089541	35468169	35468507	98.6	332	5	326
BF375312	35468061	35468355	97.6	280	5	270
BF507722	35469051	35469223	96.6	166	6	160
BM839239	35468275	35468788	99.9	511	1	509
BP290336	35468211	35468740	99.7	524	1	520
CV391258	35467630	35468147	98.3	515	2	510
DW439338	35468822	35469048	99.2	224	2	222
GD259084	35468443	35469104	100	661	0	661

TSS

No TSS is located nearby retro_hsap_105 retrocopy 5' end.

Lab

retro_hsap_105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_105 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Oryctolagus cuniculus	retro_ocun_1633
Bos taurus	retro_btau_287

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007944	1 retrocopy	retro_apla_5,
Choloepus hoffmanni	ENSCHOG00000005940	1 retrocopy	retro_chof_2,
Callithrix jacchus	ENSCJAG00000011369	1 retrocopy	retro_cjac_2033,
Ficedula albicollis	ENSFALG00000007384	1 retrocopy	retro_falb_29,
Homo sapiens	ENSG00000100170	1 retrocopy	retro_hsap_105 ,
Gallus gallus	ENSGALG00000006728	1 retrocopy	retro_ggal_2,
Monodelphis domestica	ENSMODG00000009915	1 retrocopy	retro_mdom_1324,
Mustela putorius furo	ENSMPUG00000012749	1 retrocopy	retro_mputfur_837,
Oryctolagus cuniculus	ENSOCUG00000017569	1 retrocopy	retro_ocun_1633,
Otolemur garnettii	ENSOGAG00000003370	1 retrocopy	retro_ogar_2513,
Ochotona princeps	ENSOPRG00000010458	1 retrocopy	retro_opri_6,
Procavia capensis	ENSPCAG00000015157	1 retrocopy	retro_pcap_3,
Rattus norvegicus	ENSRNOG00000017775	1 retrocopy	retro_rnor_794,
Ictidomys tridecemlineatus	ENSSTOG00000006386	1 retrocopy	retro_itri_13,