RetrogeneDB ID: retro_mmur_1306

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_4222:27666..28882(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMICG00000005448
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC5A4
• Ensembl ID: ENSMICG00000008997
• Aliases: None
• Description: solute carrier family 5 (low affinity glucose cotransporter), member 4 [Source:HGNC Symbol;Acc:11039]

Sequence

>retro_mmur_1306
GCAGACATTGCCATAGTGGCCCTGTATTTTATCCTGGTCATGTGCATTGGTTTTTTTGCCATGTGGAAATCTAATAGAAG
CACTGTGAGCGGATACTTCCTTCGCGGGGCGCTCTATGACCTGGGTGGCAATTGGTGCCTCTCTGTTTGTGAGCAATATT
GGGAGTGAGCACTTCATTGGGCTGGCAGGATCTGGAGCTGCAAGTGGATTTGCAGTGGGCGCATGGGAATTCAATGCCTT
ACTGCTTTTGCAACTTCTGGGATGGGTTTTCATCCCGATTTACATCCGGTCAGGGGTATACACGATGCCTGAATACTTGT
CCAAGCGATTTGGTGGCCATAGGATTCAGGTCTATTTTGCAGCCTTGTCTCTGATTCTCTATATCTTCACCAAGCTCTCA
GTGGATCTGTATTCGGGTGCCCTCTTTATCCAGGAGTCTTTGGGTTGGAATCTTTATGTGTCGGTCATCCTGCTCATTGG
CATGACGGCTTTGCTGACTGTCACCGGAGGCCTTGTTGCAGTGATCTACACAGACACTCTACAGGCTCTGCTCATGATCG
TTGGGGCACTTACACTTATGGTTATTAGCATGATGGAGATTGGTGGGTTTGAGGAAGTTAAGAGAAGGTACATGTTGGCC
TCACCAAATGTTACTTCCATCTTATTGACATACAACCTTTCCAACACAAATTCTTGTAATGTCCACCCTAAGAAAGAAGC
CCTGAAAATGCTGCGGGATCCAACAGATGAAGATGTTCCTTGGCCTGGATTCATTCTTGGGCAGACTCCAGCCTCAGTAT
GGTACTGGTGTGCTGACCAAGTCATCGTGCAGAGGGTCCTAGCGGCCAAAAACATTGCTCATGCCAAAGGCTCTACTCTT
ATGGCTGGCTTCTTGAAGCTTCTGCCAATGTTTATCATAGTTGTCCCAGGAATGATTTCCAGGATACTGTTTGCTGATGA
TATAGCTTGCATCAACCCAGAGCACTGCATGCAAGTGTGTGGAAGCAGAGCTGGGTGCTCCAATATTGCTTACCCACGCC
TGGTGATGAAGCTGGTTCCAGTCGGCCTTCGGGGCTTAATGATGGCAGTGATGATTGCAGCTCTGATGAGTGACTTGGAC
TCTATCTTTAACAGTGCCAGTACCATATTCACCCTTGATGTGTATAAACTCATCCGCAAGAGTGCAAGCTCCCGTGAGCT
AATGATTGTGGGGAGG

Alignment

ORF - retro_mmur_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.99 %
• Parental protein coverage: 60.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADISVIVIYFVAVMVVGLWAMLKTNRGSVGGFFL-AGRDVAWWPMGASLFASNIGSGHFVGLAGTGASSG
          ADI.....YF..VM..G..AM.K.NR..V.G.FL.AGR...W...GASLF.SNIGS.HF.GLAG.GA.SG
Retrocopy ADIAIVALYFILVMCIGFFAMWKSNRSTVSGYFL>AGRSMTWVAIGASLFVSNIGSEHFIGLAGSGAASG

Parental  IATVTFEWHSSVLLLVLGWIFVPIYIKSGVMTMPEYLKKRFGGKRLQIXXXXXXXXXXXXXXXXADIFSG
          .A....E.....LL..LGW.F.PIYI.SGV.TMPEYL.KRFGG.R.Q..................D..SG
Retrocopy FAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGHRIQVYFAALSLILYIFTKLSVDLYSG

Parental  AIFIKVALGLDLYLAIFILLAITAIYSITGGLASVIYTDTLQTIIMLIGSFILMGYAFAEVGGYKSFMEK
          A.FI...LG..LY.....L...TA....TGGL..VIYTDTLQ...M..G...LM.....E.GG.......
Retrocopy ALFIQESLGWNLYVSVILLIGMTALLTVTGGLVAVIYTDTLQALLMIVGALTLMVISMMEIGGFEEVKRR

Parental  YMNAIP---SIVEGDNLTIDARCYT-PQADSFHIFQDPVSGDIPWPGMIVGIFITSLWYWCTDQVIVQRC
          YM.A.P...SI....NL.....C...P.........DP...D.PWPG.I.G....S.WYWC.DQVIVQR.
Retrocopy YMLASPNVTSILLTYNLSNTNSCNVHPKKEALKMLRDPTDEDVPWPGFILGQTPASVWYWCADQVIVQRV

Parental  LCGKDMSHVKAACIMCGYLKLLPMFLMVMPGMISRILYTDKVACIVPSECVKQCGVEVGCSNYAYPTLVL
          L..K...H.K....M.G.LKLLPMF..V.PGMISRIL..D..ACI.P..C...CG...GCSN.AYP.LV.
Retrocopy LAAKNIAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIAYPRLVM

Parental  ELMPAGLRGLMLSVMLASLMSSLTSIFNSASTLFTMDIYTKVRKQASEKELLIAGR
          .L.P.GLRGLM..VM.A.LMS.L.SIFNSAST.FT.D.Y...RK.AS..EL.I.GR
Retrocopy KLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRKSASSRELMIVGR

Legend:

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

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1306 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1306 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007944	1 retrocopy	retro_apla_5,
Ficedula albicollis	ENSFALG00000007384	1 retrocopy	retro_falb_29,
Gallus gallus	ENSGALG00000006728	1 retrocopy	retro_ggal_2,
Microcebus murinus	ENSMICG00000008997	1 retrocopy	retro_mmur_1306 ,