RetrogeneDB ID: retro_ogar_1001

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873533.1:11052863..11053537(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSOGAG00000004389
• Aliases: None
• Description: CTD nuclear envelope phosphatase 1 [Source:HGNC Symbol;Acc:19085]

Sequence

>retro_ogar_1001
ATGATGCCGACGCAGGGTCTGCTGGGGCTGCGCACGTTTGTGGCCTTCGCGGCCAAGCTCTGGAGTTTCTTCATTTACCT
TTTGTGGAGGCAGATCCACACAGTAATTTAGTACCAAACTGTTCGATATGATATCCTCCCCTTGTCTCCTATGTCCCGGA
ATCAGCTAGCTCAGGTAAAGAGGAAGATCCCGGTGCTAAATCTGGATGAGACACTTATTCACTCCCATCATGATGGGGTC
CTGAGGCCTACAGTCCGCCTGGACACCTCCTGACTTCATTCTCAAGGTGGTAATAGACAAACATCCTGTCCGGGTTTTTG
TACACAAGAGGCCCCATGTGGATTTCTTCTTAGAATTGGTGAGCCAGTGGTATGAACCGGTGGGGTTTACAGCAAGCATG
GAAATCTATGGCTCTGCTGTGGCAGATAAACTGGACAATAGCGGAAGCATTCTCAAGAGGAGATAACTACAGACAGCACT
GCACTTTGGAGTTGGGCGGCTACATCAAGGACCTCTCTGTAGTCCACAGTGACCTCTCTTGAATTGTGATCCTGGATAAC
TCTCCAGGGGCTTACAGGAGCCATCCAGACAATGCCATCCCCATCAAATCCTGGTTCAGTGATCCCAGTGACACAGCCCT
TCTCAACCTGCCCCCAATGTTGGATGCCCTCAGA

Alignment

ORF - retro_ogar_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.23 %
• Parental protein coverage: 92.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MMRTQCLLGLRTFVAFAAKLWSFFIYLLRRQIRTVIQYQTVRYDILPLSPMSRNRLAQVKRKILVLDLDE
          MM.TQ.LLGLRTFVAFAAKLWSFFIYLL.RQI.TVI.YQTVRYDILPLSPMSRN.LAQVKRKI.VL.LDE
Retrocopy MMPTQGLLGLRTFVAFAAKLWSFFIYLLWRQIHTVI*YQTVRYDILPLSPMSRNQLAQVKRKIPVLNLDE

Parental  TLIHSHHDGVLRPTVR-PG-TPPDFILKVVIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTASMEIYG
          TLIHSHHDGVLRPTVR.PG.TPPDFILKVVIDKHPVR.FVHKRPHVDFFLE.VSQWYE.V.FTASMEIYG
Retrocopy TLIHSHHDGVLRPTVR<PG<TPPDFILKVVIDKHPVRVFVHKRPHVDFFLELVSQWYEPVGFTASMEIYG

Parental  SAVADKLDNSRSILKRR-YYRQHCTLELGSYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFS
          SAVADKLDNS.SILKRR..YRQHCTLELG.YIKDLSVVHSDLS.IVILDNSPGAYRSHPDNAIPIKSWFS
Retrocopy SAVADKLDNSGSILKRR>NYRQHCTLELGGYIKDLSVVHSDLS*IVILDNSPGAYRSHPDNAIPIKSWFS

Parental  DPSDTALLNLLPMLDALR
          DPSDTALLNL.PMLDALR
Retrocopy DPSDTALLNLPPMLDALR

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1001 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001 ,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,