RetrogeneDB ID: retro_mmur_228

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1880:128362..129162(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT13
• Ensembl ID: ENSMICG00000013917
• Aliases: None
• Description: UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13) [Source:HGNC Symbol;Acc:23242]

Sequence

>retro_mmur_228
ACACCTACAATGGTAGGAGGCCTTTTTTCTATAGACAGAGATTACTTTCAGGAAATTGGAACATATGAAGCTGGAATGGG
CATTTTGGGAGGAGAAAACCTAGAATTTCTTTTAGGATTTGGCAACATGGAGGAACTTTGGAAATTGTTACGCACTCACA
CATGGGACACGTGTTTCGAAAGCTATACCTTACACGTTTCCAGGAGGTACACAGCAGATTATCAATAAAAATAAAAGACG
ACTTGCAGAAGTGTGGATGGATGAATTCAAGAATTTCTTGTATATAATTTTTCTAGGTGTTACAAAGGTAGATTATGGAG
ATATATCATTGAGACTTGGTCTAAGACAGAAACTACAATGTAAACCTTCTCTTAATACCTAGAGAATATTTATCCTGATT
GTCAAATTCCACGTCACTATTTCTCATTGGGAGAGATACGAAATGTGGAAACAAATTGATGTCTGTATAACATTGCTAGA
AAAGAGAATGAAAAAGTTGGAATTTTTAATTGTCACAGTATGGGAGGAAATCAGGTTTTCTCTTATACTGCCAACAAAGA
AATTAGAACAGATGACCTTTGCTTGAATGTTTCCAAACTTAATGGCCCAGTCACAATGCTCAAATGCCACCACCTAAAAG
GCAACCAGCTTGGGCGTATGACCCAGTGAAATTAACCCTGCAGCATGTGAATAGTAATCAGTGCCTGGATAAAGCCACGG
AAGAGGATAGCCAGGCGCCCAGTGTTAGAGACTGCAGTGGAAGCCAGTCCCAGCAGTGGCTTCTTCAAAATGTAACCCTT

Alignment

ORF - retro_mmur_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 82.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TPTMAGGLFSIDRNYFEEIGTYDAGMDIWGGENLE-MSFRIWQCGGSLEIVTCSHVGHVFRK-ATPYTFP
          TPTM.GGLFSIDR.YF.EIGTY.AGM.I.GGENLE..SFRIWQ.GG.LEIVT.SH.GHVFRK.A.PYTFP
Retrocopy TPTMVGGLFSIDRDYFQEIGTYEAGMGILGGENLE<ISFRIWQHGGTLEIVTHSHMGHVFRK<AIPYTFP

Parental  GGTGHVINKNNRRLAEVWMDEFKDFFYIISPGVVKVDYGDVSVRKTLRENLKCKP-FSWYLENIYPDSQI
          GGT...INKN.RRLAEVWMDEFK.F.YII..GV.KVDYGD.S.R..LR..L.CKP.FS.YLENIYPD.QI
Retrocopy GGTQQIINKNKRRLAEVWMDEFKNFLYIIFLGVTKVDYGDISLRLGLRQKLQCKP<FS*YLENIYPDCQI

Parental  PRRYYSLGEIRNVETNQCLDNMGRKENEKVGIFNCHGMGGNQVFSYTADKEIRTDDLCLDVSRLNGPVIM
          PR.Y.SLGEIRNVETN.CL.N..RKENEKVGIFNCH.MGGNQVFSYTA.KEIRTDDLCL.VS.LNGPV.M
Retrocopy PRHYFSLGEIRNVETN*CLYNIARKENEKVGIFNCHSMGGNQVFSYTANKEIRTDDLCLNVSKLNGPVTM

Parental  LKCHHMRGNQL-WEYDAERLTLRHVNSNQCLDEPSEEDKMVPTMQDCSGSRSQQWLLRNMTL
          LKCHH..GNQL.W.YD...LTL.HVNSNQCLD...EED...P...DCSGS.SQQWLL.N.TL
Retrocopy LKCHHLKGNQL<WAYDPVKLTLQHVNSNQCLDKATEEDSQAPSVRDCSGSQSQQWLLQNVTL

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_228 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_228 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000011075	1 retrocopy	retro_mmur_282,
Microcebus murinus	ENSMICG00000013917	1 retrocopy	retro_mmur_228 ,
Oryctolagus cuniculus	ENSOCUG00000017645	1 retrocopy	retro_ocun_274,
Otolemur garnettii	ENSOGAG00000016208	2 retrocopies	retro_ogar_2525, retro_ogar_3272,
Tupaia belangeri	ENSTBEG00000000869	1 retrocopy	retro_tbel_1671,
Tursiops truncatus	ENSTTRG00000002506	2 retrocopies	retro_ttru_793, retro_ttru_854,