RetrogeneDB ID: retro_mluc_1777

Retrocopy location

• Organism: Microbat (Myotis lucifugus)
• Coordinates: GL429907:1840761..1841327(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPI1
• Ensembl ID: ENSMLUG00000024989
• Aliases: None
• Description: Triosephosphate isomerase [Source:UniProtKB/TrEMBL;Acc:G1Q2Y8]

Sequence

>retro_mluc_1777
CTGAACGTGGCCCACGCCGAGGTGGTTTGTGCACCAGCCACCACCTACATGGACTTCACCAGGCAGCAGCTAGATGCCGA
GATTGCCGTGACTGCTCAGAACTGCTACAGAGTGACTGATGGGGCCTTTACTGGAGAGACCAGTCCTAGCTTGATCTAAG
ACTGTGGAGCTACAGGGGTGGTCTTGAGGCAATTGAAAAGAAGGCTTGTGTTTGGGGAATCAGATGAGCTAATTTGGCAG
AAAGTGGCCCATGCCCTGGCTGAGGGACTTGGAGTGATCACTGGGGAGAAGCTAGCTGAGAGGAAAGCTGGCATCCTGAG
AAGGTCGATTTTGAACAAACCAAGGTCATTGCAGATAACATGAAGGACTGAAACAAAGTTCTTCTGGCCTATGAGCCTGT
GTGGGCCATTGGTACAGGCAAGACTGCAACACCCCAACAGGCCCAGGAAGTACACAGAAAGCTCTGGGGATGGCTTAAGT
CCAATATCTCTGATGCAGTGACTCAGACCACCTGCGTATTTATGTGGCTGGGGCAGCCTGCAAGGAGCTGCCAAGCCAGT
CTGTGT

Alignment

ORF - retro_mluc_1777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVISSSEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVMNGAFTGEISPGMIKDCGATWVVLGHSERRHV
          L.....EVVCAP.T.Y.DF.RQ.LD..IAV.AQNCY.V..GAFTGE.SP..I.DCGAT.VVL....RR.V
Retrocopy LNVAHAEVVCAPATTYMDFTRQQLDAEIAVTAQNCYRVTDGAFTGETSPSLI*DCGATGVVLRQLKRRLV

Parental  FGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGI-TEKVVFEQTKVIADNVKDWSKVVLAYEPVWAI
          FGESDELI.QKVAHALAEGLGVI...GEKL.ER.AGI..EKV.FEQTKVIADN.KD..KV.LAYEPVWAI
Retrocopy FGESDELIWQKVAHALAEGLGVIT--GEKLAERKAGI<PEKVDFEQTKVIADNMKD*NKVLLAYEPVWAI

Parental  GTGKTATPQQAQEVHEKLRGWLKSNVSDAVAQCTRIIYGGSVTGANCKELAC
          GTGKTATPQQAQEVH.KL.GWLKSN.SDAV.Q.T............C....C
Retrocopy GTGKTATPQQAQEVHRKLWGWLKSNISDAVTQTTCVFMWLGQPARSCQASLC

Legend:

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

Expression

RNA-Seq

Myotis lucifugus was not studied using RNA-Seq expression data.

ChIP-Seq

Myotis lucifugus was not studied using ChIP-Seq data.

EST

Myotis lucifugus was not studied using EST data.

TSS

Myotis lucifugus was not studied using FANTOM5 data.

Lab

retro_mluc_1777 was not experimentally validated.

Homology

Retrocopy orthology:

Myotis lucifugus 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777 , retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,