RetrogeneDB ID: retro_rnor_794

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:35834346..35835942(+)
• Located in intron of: ENSRNOG00000002010

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slc5a1
• Ensembl ID: ENSRNOG00000017775
• Aliases: Slc5a1, SGLT1
• Description: Sodium/glucose cotransporter 1 [Source:UniProtKB/Swiss-Prot;Acc:P53790]

Sequence

>retro_rnor_794
GTGCTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTGTCCTGGTCATGTGCATTGGTTTCTTTGCCATGTGGAA
ATCTAATAGAAGCACTGTGAGTGGATACTTCCTGGCCGGGCGCTCTATGACCTGGGTGGCCATTGGTGCCTCTCTGTTTG
TGAGCAATATTGGGAGTGAACACTTCATTGGGCTGGCAGGATCTGGAGCAGCCAGTGGATTTGCAGTGGGCGCATGGGAG
TTCAATGCCTTGCTGCTCTTGCAACTTCTGGGATGGGTTTTCATCCCTATTTACATCCGCTCAGGGGTGTACACCATGCC
TGAATATTTGTCCAAGAGGTTCGGTGGCCATAGGATTCAGGTCTATTTTGCGGCCTTGTCCCTGCTCCTCTATATCTTCA
CCAAGCTCTCGGTGGATCTGTACTCAGGGGCCCTCTTTATCCAGGAGTCCTTGGGTTGGAACCTTTATGTGTCTGTCATC
CTGCTCATTGGCATGACTGCTCTGCTGACCGTCACTGGAGGCCTTGTTGCAGTGATCTACACAGACACTCTCCAGGCTCT
GCTCATGATCATTGGGGCACTGACACTTATGGTTATTAGCATGATGAAGGTTGGAGGGTTTGAGGAAGTTAAGAGAAGGT
ACATGTTGGCCTCACCCAATGTTGCTTCCATTTTGTTGACACACAACCTTTCCAACACAAATTCTTGTATGGTGCATCCT
AAGGCAGATGCCCTAAAGATGTTGAGAGATCCAACAGATGAAGACGTCCCATGGCCTGGATTCATTCTTGGGCAGACCCC
AGCCTCGGTATGGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTTCTAGCAGCCAAAAACATTGCTCATGCCAAAG
GTTCTACTCTGATGGCTGGCTTCTTGAAGCTCCTACCAATGTTTATCATAGTCGTACCCGGAATGATTTCCAGGATACTG
TTTGTTGATGATATAGCTTGCATCAACCCAGAACACTGCATGCAAGTGTGTGGAAGCAGAGCTGGGTGCTCCAATATTGC
TTACCCACGCCTGGTGATGGAGTTGGTTCCCGTGGGCCTTCGGGGCCTGATGATGGCAGTGATGATTGCAGCTCTGATGA
GCGACTTGGACTCCATCTTTAACAGCGCCAGTACCATATTCACCCTCGATGTGTACAAGCTTCTCCGCAACAATGCAAGC
TCGCGGGAACTGATGATTGTGGGCAGGATATTTGTGGCTTTTATGGTTGTCATCAGCATAGCATGGGTGCCAATTATTGT
GGAGATGCAAGGAGGCCAAATGTACCTTTATATCCAGGAGGTGGCGGATTATCTGACCCCTCCGGTGGCGGCCCTCTTCC
TTCTGGCAATTTTCTGGAAACGTTGCAATGAGCAAGGGGCTTTCTATGGTGGAATGGCAGGTTTTGTTCTTGGAGCTATC
CGTTTGATACTGGCTTTCACCTACCGTGCTCCTGAGTGTGACCAACCTGATAACAGGCCCAGCTTCATCAAAGACATCCA
TTATATGTATGTGGCTACAGCATTATTTTGGATCACAGGACTCATTACTGTAATTGTTAGTCTTCTCACACCACCT

Alignment

ORF - retro_rnor_794 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 79.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRNAADISVIVIYFVVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGLAGTGA
          ....ADI.....YFV.VM..G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SNIGS.HF.GLAG.GA
Retrocopy VLETADIAIVALYFVLVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGA

Parental  AAGIAMGGFEWNALVFVVVLGWLFVPIYIKAGVVTMPEYLRKRFGGKRIQIYLSVLSLLLYIFTKISADI
          A.G.A.G..E.NAL.....LGW.F.PIYI..GV.TMPEYL.KRFGG.RIQ.Y...LSLLLYIFTK.S.D.
Retrocopy ASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLLLYIFTKLSVDL

Parental  FSGAIFINLALGLDIYLAIFILLAITALYTITGGLAAVIYTDTLQTAIMLVGSFILTGFAFREVGGYEAF
          .SGA.FI...LG...Y.....L...TAL.T.TGGL.AVIYTDTLQ...M..G...L.......VGG.E..
Retrocopy YSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIIGALTLMVISMMKVGGFEEV

Parental  MDKYMKAIPTLVS---DGNITVKEECYT-PRADSFHIFRDPITGDMPWPGLIFGLSILALWYWCTDQVIV
          ...YM.A.P...S.....N......C...P.AD.....RDP...D.PWPG.I.G......WYWC.DQVIV
Retrocopy KRRYMLASPNVASILLTHNLSNTNSCMVHPKADALKMLRDPTDEDVPWPGFILGQTPASVWYWCADQVIV

Parental  QRCLSAKNMSHVKAGCTLCGYLKLLPMFLMVMPGMISRILYTDKIACVLPSECKKYCGTPVGCTNIAYPT
          QR.L.AKN..H.K......G.LKLLPMF..V.PGMISRIL..D.IAC..P..C...CG...GC.NIAYP.
Retrocopy QRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFVDDIACINPEHCMQVCGSRAGCSNIAYPR

Parental  LVVELMPNGLRGLMLSVMMASLMSSLTSIFNSASTLFTMDIYTKIRKGASEKELMIAGRLFILVLIGISI
          LV.EL.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y...R..AS..ELMI.GR.F......ISI
Retrocopy LVMELVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLLRNNASSRELMIVGRIFVAFMVVISI

Parental  AWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFCKRVNEPGAFWGLILGFLIGISRMITEFAYGT
          AWVPI....Q.GQ...YIQ....YL.PP.AA.FLLAIF.KR.NE.GAF.G...GF..G..R.I..F.Y..
Retrocopy AWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAIRLILAFTYRA

Parental  GSCMEPSNCPKIICGVHYLYFAIILFAISVVTVLVISLLTKP
          ..C..P.N.P..I...HY.Y.A..LF.I........SLLT.P
Retrocopy PECDQPDNRPSFIKDIHYMYVATALFWITGLITVIVSLLTPP

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
SRP017611_brain	2.73 RPM	0.07 RPM
SRP017611_kidney	10.05 RPM	44.03 RPM
SRP017611_liver	0.74 RPM	0.67 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_rnor_794 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG374293	35835100	35835465	100	365	0	365
CA513484	35834269	35834974	99.8	703	2	701

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_794 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_200

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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,