RetrogeneDB ID: retro_itri_13

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:8293206..8295363(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000014257
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC5A1
• Ensembl ID: ENSSTOG00000006386
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 [Source:HGNC Symbol;Acc:11036]

Sequence

>retro_itri_13
ATGAGGGCTGTTCTGGAGACAGCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTGATGTGCATTGGTTTTTTTGC
CATGTGGAAATCTAATAGAAGCACCGTGAGTGGATACTTCCTGGCGGGGCGCTCTATGACCTGGGTAGCAATTGGTGCCT
CTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGC
GCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTTTGGGATGGGTTTTTATCCCAATTTACATCCGGTCGGGGGTATA
CACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTTGCAGCCCTGTCTCTGATTCTCT
ATATCTTCACCAAGCTCTCAGTGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAACCTCTATGTG
TCTGTCATCCTGCTCATTGGTATGACTGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTTATCTACACAGACACTCT
GCAGGCTCTGCTCATGATTGTTGGGGCACTCACACTTATGATTATTAGCATGATGGAGATTGGTGGGTTTGAGGAAGTTA
AGAGAAGGTACATGTTGGCCTCACCTAATATCCCTTCCATCTTGTTGACATACAACCTATCAAACACAAATTCTTGTAAC
GTCAACCCTAAGAAAGAAGCCCTAAAAATGTTGCGGGATCCAACAGATGAAGATGTTCCATGGCCCGGATTCATCCTTGG
GCAGACCCCAGCCTCAGTGTGGTACTGGTGTGCTGACCAAGTCATCGTACAAAGGGTCCTGGCAGCCAAAAACATTGCTC
ACGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTGAAGCTTCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCC
AGGATACTGTTTACTGATGATATAGCTTGCATCAACCCAGAGCACTGCATGCAAGTGTGTGGAAGCCGAGCTGGGTGCTC
CAATATTGCTTACCCACGCCTGGTGATGAAGCTTGTTCCTGTGGGCCTTCGGGGGTTGATGATGGCTGTGATGATTGCAG
CTCTAATGAGTGACTTGGACTCTATATTTAACAGTGCCAGTACTATATTCACTCTTGATGTGTACAAACTCATCCGCAAG
AGTGCAAGCTCCCGGGAACTAATGATTGTGGGGAGGATATTTGTGGCTTTTATGGTGGTGATCAGCATAGCATGGGTACC
AATCATTGTGGAGATGCAAGGTGGCCAGATGTACCTTTACATTCAGGAGGTAGCAGATTACCTGACCCCCCCAGTGGCGG
CCCTATTCCTTTTGGCAATTTTCTGGAAGCGCTGCAATGAACAAGGGGCTTTCTATGGTGGAATGGCTGGCTTTGTTCTT
GGAGCAGTCCGTTTGATACTGGCCTTTGCCTACCGTGCCCCGGAGTGTGACCAACCTGATAATAGACCAGGCTTCATCAA
AGACATCCATTATATGTATGTGGCCACGGCATTGTTTTGGGTCACAGGACTCATTACTGTAATTGTCAGCCTTCTCACTC
CACCTCCCACAAAGGAACAGATTCGCACCACCACCTTTTGGTCTAAGAAGAACCTGGTGACAAAGGAAAGCTGCTCTCAG
AAAGATGAGCCATACAAAATGCAGGAGAAGAGCATTCTGCGATGCAGTGAGAACAGTGAGGCCATCATCCATGTCATTCC
CAATGGGAAATCTGAAGATAGTATTAAGGGCCTTCAGCCTGAAGATGTCAATCTTTTGGTGACCTGCAGAGAGGAGGGTA
ACCCTGTGGCTTCCTTGGGTCATTCAGAGGCAGAAACACCAGTAGATACTTATTCCAATGGGCAAGCGGCTCTCATGGGT
GAGAAAGAGAGAAAGAAAGAAACAGAGGATAGAAGCCGGTACTGGAAGTTCATAGACTGGTTTTGTGGCTTTAAAAGTAA
GAGCATCAGCAAGAGGAGTCTCAGAGACTTGATGGAGGAGGAGGCTGTCTGTTTACAAATGTTAGAAGAGACTCCACAAG
TTAAAGTCATACTAAATATTGGACTTTTTGCTGTGTGTTCTCTTGGAATTTTCATGTTTGTTTATTTCTCCATATGA

Alignment

ORF - retro_itri_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.64 %
• Parental protein coverage: 79.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

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

Parental  ASGIATGAFEWNALFLVVVLGWIFVPIYIKAGVVTMPEYLRKRFGGKRIQIYLSVLSLLLYIFTKISADI
          ASG.A.GA.E.NAL.L...LGW.F.PIYI..GV.TMPEYL.KRFGG.RIQ.Y...LSL.LYIFTK.S.D.
Retrocopy ASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDL

Parental  FSGAIFINLALGLDIYLAIFILLAITGLYTITACVGGLAAVIYTDTLQTAIMLVGSFILTGFAFNEVGGY
          .SGA.FI...LG...Y.....L...T.L.T.T...GGL.AVIYTDTLQ...M.VG...L......E.GG.
Retrocopy YSGALFIQESLGWNLYVSVILLIGMTALLTVT---GGLVAVIYTDTLQALLMIVGALTLMIISMMEIGGF

Parental  EAFMEKYMKA---IPTLISDGNTTIKEEC-YTPREDSFHIFRDPLKGDLPWPGLIFGLAILALWYWCTDQ
          E.....YM.A...IP......N......C...P........RDP...D.PWPG.I.G......WYWC.DQ
Retrocopy EEVKRRYMLASPNIPSILLTYNLSNTNSCNVNPKKEALKMLRDPTDEDVPWPGFILGQTPASVWYWCADQ

Parental  VIVQRCLSAKNMSHVKAGCTLCGYMKLLPMFLMVMPGMISRILYTEKIACVIPSECKKYCGTPVGCTNIA
          VIVQR.L.AKN..H.K......G..KLLPMF..V.PGMISRIL.T..IAC..P..C...CG...GC.NIA
Retrocopy VIVQRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFTDDIACINPEHCMQVCGSRAGCSNIA

Parental  YPTLVVELMPNGLRGLMLSVMMASLMSSLTSIFNSASTLFTMDIYTKIRKQASEKELMIAGRLFILFLIA
          YP.LV..L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y..IRK.AS..ELMI.GR.F..F...
Retrocopy YPRLVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGRIFVAFMVV

Parental  ISIAWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAVFWKRITEPGAFWGLILGFLIGISRMITEFA
          ISIAWVPI....Q.GQ...YIQ....YL.PP.AA.FLLA.FWKR..E.GAF.G...GF..G..R.I..FA
Retrocopy ISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFVLGAVRLILAFA

Parental  YGTGSCMEPSNCPTIICGVHYLYFAIILFVISVITIVVISLFTKP
          Y....C..P.N.P..I...HY.Y.A..LF.......V..SL.T.P
Retrocopy YRAPECDQPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPP

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_13 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_13 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 ,