RetrogeneDB ID: retro_ocun_1633

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018729:892084..893722(+)
• Located in intron of: ENSOCUG00000025692

Retrocopy information

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

Parental gene information

• Parental gene symbol: RA_M004_JSM9082BF
• Ensembl ID: ENSOCUG00000017569
• Aliases: None
• Description: solute carrier family 5 (sodium/glucose cotransporter), member 1 (SLC5A1), mRNA [Source:RefSeq mRNA;Acc:NM_001101692]

Sequence

>retro_ocun_1633
CTGTCATTGGACACTTACTCACAAGTTACCAGAATGAGGGCTGTACTGGAGACAGCAGACATTGCCATAGTGGCCCTGTA
TTTTATCCTGGTCATGTGCATTGGTTTTTTTGCCATGTGGAAATCTAATAGAAGCACCGTAAGTGGATACTTCCTGGCGG
GGCGCTCTATGACCTGGGTAGCGATTGGTGCCTCTCTGTTTGTGAGCAATATTGGGAGTGAGCACTTCATTGGGCTGGCA
GGATCTGGAGCTGCAAGTGGATTTGCAGTGGGCGCATGGGAATTCAATGCCTTACTGCTTTTGCAACTTCTGGGATGGGT
TTTCATCCCGATTTACATCCGGTCAGGGGTATACACCATGCCTGAATACTTGTCCAAGCGATTTGGTGGCCATAGGATTC
AGGTCTATTTTGCAGCCTTGTCTCTGCTTCTCTATATCTTCACCAAGCTCTCAGTGGATCTGTATTCAGGTGCCCTCTTT
ATCCAGGAGTCTTTGGGTTGGAACCTTTATGTGTCTGTCATCCTGCTCATTGGCATGACTGCTTTGCTGACTGTCACCGG
AGGCCTTGTTGCAGTGATCTACACAGACACTCTACAGGCTCTGCTCATGATTGTTGGGGCACTCACACTTATGATTATCA
GCATGATGGAGGTTGGCGGGTTTGAGGAAGTTAAGAGAAGGTACATGTTGGCCGCACCCAATGTCACCTCCATCTTGTTG
ACATACAACCTTTCCAACACAAATTCTTGTAATGTCCAACCTAAGAAAGACGCCTTGAAGATGTTGCGGAATCCAACAGA
TGAAGATGTTCCGTGGCCTGGATTCATTCTTGGGCAGACCCCAGCCTCAGTGTGGTATTGGTGTGCTGACCAAGTCATCG
TGCAGAGGGTCTTGGCTGCCAAAAACATTGCTCATGCCAAAGGCTCTACTCTTATGGCTGGCTTCTTGAAGCTTCTGCCA
ATGTTTATCATAGTGGTCCCAGGAATGATTTCCAGGATACTGTTTGCTGACGATCTAGCTTGCATCAACCCGGAGCACTG
CATGCAAGTGTGCGGGAGCCGAGCCGGGTGTTCCAATATTGCTTACCCGCACCTGGTGATGAAGCTGGTTCCCGTGGGCC
TTCGGGGCTTGATGATGGCAGTGATGATCGCAGCGCTAATGAGTGACCTGGACTCTATCTTTAACAGTGCCAGCACCATA
TTCACCCTGGACGTGTACAAACTCATCCGCAAGAGCGCCAGTTCTCGGGAGCTGATGATCGTGGGGAGGATATTTGTGGC
TTTTATGGTGGTTATCAGCATAGCATGGGTGCCAATCATCGTGGAAATGCAAGGAGGCCAGATGTACCTTTACATTCAGG
AGGTAGCAGATTACCTGACACCTCCAGTGGCAGCCCTGTTTCTTCTGGCAATTTTCTGGAAGCGTTGCAATGAGCAAGGG
GCTTTCTATGGCGGAATGGCTGGATTTGTTCTTGGAGCAGTCCGTTTGGTACTGGCCTTTACATACCGCGCCCCAGAATG
CGACCAGCCTGATAACAGACCTGGTTTCATCAAAGACATCCACTATATGTATGTGGCCACAGCACTGTTTTGGGTCACAG
GACTCATTACTGTAATTGTTAGCCTTCTTACCCCACCT

Alignment

ORF - retro_ocun_1633 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.3 %
• Parental protein coverage: 81.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LATSTAAPLESYERIRNAADISVIVIYFLVVMAVGLWAMFSTNRGTVGGFFLAGRSMVWWPIGASLFASN
          L...T.............ADI.....YF..VM..G..AM...NR.TV.G.FLAGRSM.W..IGASLF.SN
Retrocopy LSLDTYSQVTRMRAVLETADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFLAGRSMTWVAIGASLFVSN

Parental  IGSGHFVGLAGTGAASGIATGGFEWNALIMVVVLGWVFVPIYIRAGVVTMPEYLQKRFGGKRIQIYLSIL
          IGS.HF.GLAG.GAASG.A.G..E.NAL.....LGWVF.PIYIR.GV.TMPEYL.KRFGG.RIQ.Y...L
Retrocopy IGSEHFIGLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAAL

Parental  SLLLYIFTKISADIFSGAIFIQLTLGLDIYVAIIILLVITGLYTITGGLAAVIYTDTLQTAIMMVGSVIL
          SLLLYIFTK.S.D..SGA.FIQ..LG...YV..I.L...T.L.T.TGGL.AVIYTDTLQ...M.VG...L
Retrocopy SLLLYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTL

Parental  TGFAFHEVGGYEAFTEKYMRA---IPSQISYGNTSIPQKCYT-PREDAFHIFRDAITGDIPWPGLVFGMS
          ......EVGG.E.....YM.A.....S.....N.S....C...P..DA....R.....D.PWPG...G..
Retrocopy MIISMMEVGGFEEVKRRYMLAAPNVTSILLTYNLSNTNSCNVQPKKDALKMLRNPTDEDVPWPGFILGQT

Parental  ILTLWYWCTDQVIVQRCLSAKNLSHVKAGCILCGYLKVMPMFLIVMMGMVSRILYTDKVACVVPSECERY
          ....WYWC.DQVIVQR.L.AKN..H.K......G.LK..PMF.IV..GM.SRIL..D..AC..P..C...
Retrocopy PASVWYWCADQVIVQRVLAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDLACINPEHCMQV

Parental  CGTRVGCTNIAFPTLVVELMPNGLRGLMLSVMMASLMSSLTSIFNSASTLFTMDIYTKIRKKASEKELMI
          CG.R.GC.NIA.P.LV..L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y..IRK.AS..ELMI
Retrocopy CGSRAGCSNIAYPHLVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMI

Parental  AGRLFMLFLIGISIAWVPIVQSAQSGQLFDYIQSITSYLGPPIAAVFLLAIFWKRVNEPGAFWGLVLGFL
          .GR.F..F...ISIAWVPI....Q.GQ...YIQ....YL.PP.AA.FLLAIFWKR.NE.GAF.G...GF.
Retrocopy VGRIFVAFMVVISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFV

Parental  IGISRMITEFAYGTGSCMEPSNCPTIICGVHYLYFAIILFVISIITVVVVSLFTKP
          .G..R....F.Y....C..P.N.P..I...HY.Y.A..LF.......V.VSL.T.P
Retrocopy LGAVRLVLAFTYRAPECDQPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPP

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	9.38 RPM	0.99 RPM
SRP017611_kidney	66.19 RPM	160.75 RPM
SRP017611_liver	1.62 RPM	4.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1633 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1633 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1633 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_105
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,