RetrogeneDB ID: retro_mmur_164

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_153:52076..52772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSMICG00000008449
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_mmur_164
CAGTCAGCTAAGTCACCTACTGCAACCTTTGAGAAACACGGAGAGCACCTACCCCGAGGAGAAGGTAGATTTGGAGTAAG
CCGTCGTCGACATAATTCCTCTGATGGCTTTTTTAACAATGGACCCCTACGAACTACAGGAGATTCCTGGCACCAGCCTT
CTCTGTTCCGCCATGATTCTGTGGACTCTGGTGTCTCTAAGGGAGCATATGCTGGAATCACAGGGAACCCATCTTATTGG
TATGGCTCTTCCCGAGGTCACGATGTTATGAGCCAGCGTAGTGGAGGTGGCACAGGGAACCATCGCCATTGGAATGGCAG
CTTCCACTCCCAGAAAGGCTGTTCCTTTCAGGAAAGGCCACCTACAGAGATTAGGGAAGAAAAGAAAGAAGACAAGGTGG
AAAAGTTGCAGTTTGAAGAAGAAGACTTTCCTTCTTTGAATCCAGAAGCTGGCAAACAGAATCAGCCATGCAGACCTTTT
GGGACCCCTTTTGGAGTGTGGGAAAACCCACCTAGTGCCAAGCAACCCTCCAAAATGATAGTTATCAAAAAAGTATCCAA
AGAGGATCCTGCTGCTGCCTTCTCTGCTGCATTCACCTCACCAGGATCTCACCATGCAAATGGGAATAAATCATCATCCA
TAGTTCCAAGTGTCTATAAGAACCTGGTTCCTAAGCCTGCACCACCTCCTTCTAAG

Alignment

ORF - retro_mmur_164 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.95 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSAKSPTATFEKHGEHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTGDSWHQPSLFRHDSVDSGVSKGAY
          QSAKSPTATFEKHGEHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTGDSWHQPSLFRHDSVDSGVSKGAY
Retrocopy QSAKSPTATFEKHGEHLPRGEGRFGVSRRRHNSSDGFFNNGPLRTTGDSWHQPSLFRHDSVDSGVSKGAY

Parental  AGITGNPSYWYGSSRGHDVMSQRSGGGTGNHRHWNGSFHSRKGCSFQERPPTEIREEKKEDKVEKLQFEE
          AGITGNPSYWYGSSRGHDVMSQRSGGGTGNHRHWNGSFHS.KGCSFQERPPTEIREEKKEDKVEKLQFEE
Retrocopy AGITGNPSYWYGSSRGHDVMSQRSGGGTGNHRHWNGSFHSQKGCSFQERPPTEIREEKKEDKVEKLQFEE

Parental  EDF-FFDPAKQNQCRP---FGXXXXXXXNPPSAKQPSKMIVIKKVSKEDPAAAFSAAFTSPGSHHANGNK
          EDF....P....Q..P...FG.......NPPSAKQPSKMIVIKKVSKEDPAAAFSAAFTSPGSHHANGNK
Retrocopy EDFPSLNPEAGKQNQPCRPFGTPFGVWENPPSAKQPSKMIVIKKVSKEDPAAAFSAAFTSPGSHHANGNK

Parental  SSSIVPSVYKNLVPKPAPPPSK
          SSSIVPSVYKNLVPKPAPPPSK
Retrocopy SSSIVPSVYKNLVPKPAPPPSK

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_164 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_164 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164 ,
Microcebus murinus	ENSMICG00000014678	1 retrocopy	retro_mmur_1198,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243,