RetrogeneDB ID: retro_opri_6

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_635:71566..73723(+)
• Located in intron of: ENSOPRG00000018417

Retrocopy information

• Ensembl ID: ENSOPRG00000008608
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSOPRG00000010458
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 [Source:HGNC Symbol;Acc:11036]

Sequence

>retro_opri_6
ATGAGGGCTGTACTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGGTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTAAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCCATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCGGCAAGCGGATTCGCAGTGGGT
GCTTGGGAGTTCAATGCCTTACTGCTTTTGCAACTTTTGGGATGGGTTTTCATCCCAATTTACATCCGGTCGGGGGTATA
CACCATGCCTGAATACTTGTCCAAGCGATTCGGTGGCCATAGGATTCAGGTCTACTTTGCAGCCTTGTCTCTGATTCTCT
ATATCTTCACCAAGCTCTCAGTGGATCTGTATTCAGGCGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTTTATGTG
TCTGTCATCCTGCTCATTGGCATGACTGCTTTACTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACCTT
ACAGGCCCTGCTCATGATTGTTGGGGCCCTCACACTTATGATTATAAGCATGATGGAGGTTGGCGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCCAACGTCACGTCCATCTTGTTGACATACAACCTTTCAAACACAAATTCTTGTAAT
GTCCAGCCTAAGAAAGATGCCTTGAAAATGTTGAGGAATCCAACAGATGAAGATGTTCCGTGGCCTGGATTCATACTTGG
ACAGACCCCCGCCTCAGTGTGGTATTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTCCTAGCTGCCAAAAACATTGCTC
ATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTGAAGCTTCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGGATACTGTTTGCTGATGATCTAGCTTGCATCAACCCAGAGCACTGCATGCAGGTGTGTGGAAGCAGAGCCGGGTGCTC
TAATATCGCTTACCCACACCTGGTGATGAAGCTGGTTCCTGTGGGCCTTCGGGGCTTAATGATGGCGGTGATGATTGCAG
CTCTCATGAGTGACCTGGACTCTATCTTTAACAGTGCCAGTACCATATTCACCCTTGATGTGTACAAACTCATCCGCAAG
AGTGCAAGTTCCCGGGAGCTAATGATTGTGGGGAGGATATTTGTGGCTTTTATGGTGGTTATCAGCATAGCATGGGTGCC
GATCATCGTGGAGATGCAAGGAGGCCAGATGTACCTTTACATCCAGGAGGTGGCAGATTACCTGACACCTCCGGTGGCAG
CCCTGTTCCTTCTGGCAATTTTCTGGAAGCGCTGCAATGAACAAGGGGCTTTCTACGGAGGAATGGCTGGATTTGTGCTT
GGAGCAGTCCGTTTGATACTGGCTTTTACATACCGTGCCCCGGAATGTGACCAGCCTGATGAGAGACCCAGTTTCATCAA
AGACATCCATTACATGTATGTGGCCACAGCATTGTTCTGGATCACAGGACTCATTACTGTGATTGTTAGCCTCCTCACCC
CACCTCCCACGAAGGAGCAGATTCGCACCACCACCTTTTGGTCCAAGAAGAACCTGGTGGTGAAGGAGAGCTGCTCTGCC
AGAGAGGAACTGTACAAAATGCAGGAGAAGAGCATGCTGAAGTGCAGTGAGAATAGTGAGGCCATCAACCACATCATTCC
CAATGGGAAATCTGAAGATAGCATCAAAGGCCTTCAGCCAGAAGACGTCAATCTGTTGGTGACCTGCCGAGAGGAGGCCA
ACCCAGTGGCATCCGTGGGCCACTCTGAGGCAGAAACACCAGTAGATGCTTATTCCAATGGGCAAGCAGCTCTCATGGGA
GAGAAAGAGAGAAAGAAGGAAATGGAGGCTGGCAGCCGCTACTGGAAGTTCATAGACTGGTTTTGCGGCTTTAAGAGTAA
GAGTGTCAGCAAGAGGAGTCTCAGAGACCTCATGGAGGAGGAGGCTGTTTGTTTACAGATGTTAGAGGAGACTCCCAGAG
TAAAGCTGATACTCAACGTTGGACTTTGTGCTGTGTGTTCACTTGGAATTTTCATGTTTGTCTATTTCTCCTTATGA

Alignment

ORF - retro_opri_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 79.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRNAADISVIVIYFLVVLAVGLWAMLSTNRGTVGGFFLAGRSMVWWPIGASLFASNIGSGHFVGLAGTGA
          ....ADI.....YF..V...G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SNIGS.HF.GLAG.GA
Retrocopy VLETADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSNIGSEHFIGLAGSGA

Parental  ASGIATGGFEWNALIMVIVLGWVFVPIYIKAGVVTMPEYLQKRFGGKRIQIYLSVLSLLIYIFTKISADI
          ASG.A.G..E.NAL.....LGWVF.PIYI..GV.TMPEYL.KRFGG.RIQ.Y...LSL..YIFTK.S.D.
Retrocopy ASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDL

Parental  FSGAIFIQLALGLDLYVAIIVLLVITGIFTITGGLSAVIYTDALQTLIMLVGSCILVGFAFHEVGGYDAF
          .SGA.FIQ..LG..LYV..I.L...T...T.TGGL.AVIYTD.LQ.L.M.VG...L......EVGG....
Retrocopy YSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMIISMMEVGGFEEV

Parental  TEKYMQAIP---SVTSEGNFSASQECYT-PREDAFHIFRDAITGDIPWPGLVFGMSILTLWYWCTDQVIV
          ...YM.A.P...S.....N.S....C...P..DA....R.....D.PWPG...G......WYWC.DQVIV
Retrocopy KRRYMLASPNVTSILLTYNLSNTNSCNVQPKKDALKMLRNPTDEDVPWPGFILGQTPASVWYWCADQVIV

Parental  QRCLSAKNMSHVKAGCIMCGYLKILPMFLIIMMGMISRILYTDRIACVVPSECERYCGTRVGCTNIAFPI
          QR.L.AKN..H.K....M.G.LK.LPMF.I...GMISRIL..D..AC..P..C...CG.R.GC.NIA.P.
Retrocopy QRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDLACINPEHCMQVCGSRAGCSNIAYPH

Parental  LVVELMPNGLRGLMLSVMMASLISSLTSVFNSASTLFTMDLYTKIRNKASERELMIVGRVFMLFLIAVSI
          LV..L.P.GLRGLM..VM.A.L.S.L.S.FNSAST.FT.D.Y..IR..AS.RELMIVGR.F..F....SI
Retrocopy LVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVVISI

Parental  AWVPIVQSAQSGQLFDYIQSITSYLGPPIAALFLLAIFWKRTNEPGAFWGLIFGFLVGISRMIAEFAYGT
          AWVPI....Q.GQ...YIQ....YL.PP.AALFLLAIFWKR.NE.GAF.G...GF..G..R.I..F.Y..
Retrocopy AWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLILAFTYRA

Parental  GSCVEPSNCPTIICGVHYLYFAIILFVISIIVTVAVSLFTKP
          ..C..P...P..I...HY.Y.A..LF.I....TV.VSL.T.P
Retrocopy PECDQPDERPSFIKDIHYMYVATALFWITGLITVIVSLLTPP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_6 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,