RetrogeneDB ID: retro_mmur_1130

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_24459:6110..6678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: T
• Ensembl ID: ENSMICG00000016122
• Aliases: None
• Description: T, brachyury homolog (mouse) [Source:HGNC Symbol;Acc:11515]

Sequence

>retro_mmur_1130
TTTGCCAAAGTCAAACTCACCAAAGAACTCAACAGAGGTGTCAGATCATGTTGACCTCCTTATATAAATATGAACCTCAA
TCCACATATTGAGAGTTGAGGGTCCAGAGGGGATCACTAGCCATTGTATTCCCAAGACCCAATACATATTTTTCAAGGCT
GATCAGAATCATCGGGAATTATGCCTCTTATAGTTAGATACAATTCCTTCACAAAGGCTTTTCTTCTTGCAAAGAAAAGC
AGTGATCACAAAGACATGATGGAAGAACCTGGAGACAAACAGCAATCTGGTTATTCTTAATGAAAATGGCTCATTCCTAG
AACCAGTACCCCTGTCCACCTGCCAGCAACCACTCTCATCCACTTCTCGTGCTTTCCTTTCTACATGGCTGAGAAAGAAA
CTCTGTCCTGAGGAACCACTGTTCATACCCACACACATATTGGAACAGTTCTCCAACCATTCTGACAAGTCATTTGCATG
TTATCCATTCTCCAATCCTGTGGTAATTCGGTCCAGCCTCAGAATGTCTGTGCATGTGAGCACACTACCCACAATTCACA
CAGAAGGA

Alignment

ORF - retro_mmur_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.9 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  FSKVKLTNKLNGGG-QIMLNSLHKYEPR-IHIVRVGAPQRMITSHCFPETQFIAVTAYQN-EEITALKIK
          F.KVKLT..LN.G..QIML.SL.KYEP..IHI.RV..P...ITSHC.P.TQ.I...A.QN..E...L...
Retrocopy FAKVKLTKELNRGV<QIMLTSLYKYEPQ<IHILRVEGPEG-ITSHCIPKTQYIFFKADQNHRELCLL*LD

Parental  YNP-FAKAFLDAKERSDHKDMLEEPGDSQQAGYSQWGWLIPGTSS-LCPPANPHAQFGGPLPLPPTHGCE
          ..P.F.KAFL.AK..SDHKDM.EEPGD.QQ.GYS...WLIP.TS...CPPA..H......L.L...HG.E
Retrocopy TIP<FTKAFLLAKKSSDHKDMMEEPGDKQQSGYS**KWLIPRTST<PCPPASNHSH--PLLVLSFLHG*E

Parental  RYPALRSHRSSYPSPYVHRNSSPT-YSDNSSAC-LSMLQSHDN-WSSLGMPAHTGMLPVGHNAG
          R...LR.H..SYP..Y...NSSPT..SD.S.AC.LS.LQS..N..SSL.M..H...LP..H..G
Retrocopy RNSVLRNH-CSYPHTY--WNSSPT<HSDKSFAC<LSILQSCGN>RSSLRMSVHVSTLPTIHTEG

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_1130 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1130 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
Choloepus hoffmanni	ENSCHOG00000006236	1 retrocopy	retro_chof_209,
Equus caballus	ENSECAG00000007994	1 retrocopy	retro_ecab_568,
Microcebus murinus	ENSMICG00000016122	1 retrocopy	retro_mmur_1130 ,
Nomascus leucogenys	ENSNLEG00000011552	1 retrocopy	retro_nleu_1501,