RetrogeneDB ID: retro_ogar_2846

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873672.1:1186005..1186727(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF3
• Ensembl ID: ENSOGAG00000015569
• Aliases: None
• Description: polycomb group ring finger 3 [Source:HGNC Symbol;Acc:10066]

Sequence

>retro_ogar_2846
ATGCTGACCAGGAAGGTCAGGCTATGGGACATCAAAGCCCACATCACTTGCCACCTATGCAGCGGGTACCTCATCAACGC
AACCACGGGGATAAGTGTCTGCACATGTTCTGCCAGAGTTGCCTGGTGAACTATTTGGAAGAGAATAACACCTGCCCGAC
CTGTCGGATCATGATCCACCAGAGCTACCCGCTGCAGTACACCGGTCATGACAGAACCATGCAGGACATTGTTTACAAGT
TGGTATCAGGCCTCCAGGAAGCGGAGATGAAAAAGCAGAGAGAATTCTACCACAAACTGGGCATGGAGGTGCCTGGCGAC
ATCAAGGGAGAGGCCTGCTCTGCGAAGCAGCATGTGGACCCCCACCGCAGCGGTGAAACCAAAGCAGACCACAGTTCAAA
CAAAGAGGCAGCGGAGGAGAAACCGGAGGAGGACCATGACTACCACAGGAGCGAGGAGCAGGTGAGCATCTGTCTGGAGT
GCAACAGCAGCAAACTGCCCAGGCTGAAACGGAAGTGGATCCGCTGCTCTGCCCAGGCCACTGTGTTGCACCTGAAGAAG
TTCATCGCCAAGAAGCTTAACCTGTCATCCTTCAATGAGCTGGACATCTTATGCGATGAGGACACTGGGCAAGGACCACA
CACTCAAGTCGTGGTTGTCATGAGGTAGAGATTCAAGAAGGCGCCCCTGCTGCTGTACTACAGACCCAAGATGGACTTGC
TG

Alignment

ORF - retro_ogar_2846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLTRKVRLWDINAHITCRLCSGYLIDATTVT-ECLHTFCRSCLVKYLEENNTCPTCRIVIHQSHPLQYIG
          MLTRKVRLWDI.AHITC.LCSGYLI.ATT....CLH.FC.SCLV.YLEENNTCPTCRI.IHQS.PLQY.G
Retrocopy MLTRKVRLWDIKAHITCHLCSGYLINATTGI<KCLHMFCQSCLVNYLEENNTCPTCRIMIHQSYPLQYTG

Parental  HDRTMQDIVYKLVPGLQEAEMRKQREFYHKLGMEVPGDVKGEACSAKQHVDPHRNGETKADDSSNKEAAE
          HDRTMQDIVYKLV.GLQEAEM.KQREFYHKLGMEVPGD.KGEACSAKQHVDPHR.GETKAD.SSNKEAAE
Retrocopy HDRTMQDIVYKLVSGLQEAEMKKQREFYHKLGMEVPGDIKGEACSAKQHVDPHRSGETKADHSSNKEAAE

Parental  EKPEEDHDYHRSDEQVSICLECNSSKLRGLKRKWIRCSAQATVLHLKKFIAKKLNLSSFNELDILCNEEI
          EKPEEDHDYHRS.EQVSICLECNSSKL..LKRKWIRCSAQATVLHLKKFIAKKLNLSSFNELDILC.E..
Retrocopy EKPEEDHDYHRSEEQVSICLECNSSKLPRLKRKWIRCSAQATVLHLKKFIAKKLNLSSFNELDILCDEDT

Parental  LGKDHTLKFVVVTRWRFKKAPLLLHYRPKMDLL
          ....HT...VVV.R.RFKKAPLLL.YRPKMDLL
Retrocopy GQGPHT-QVVVVMR*RFKKAPLLLYYRPKMDLL

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_2846 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707,
Macaca mulatta	ENSMMUG00000012624	1 retrocopy	retro_mmul_2182,
Monodelphis domestica	ENSMODG00000005677	3 retrocopies	retro_mdom_1481, retro_mdom_885, retro_mdom_985,
Nomascus leucogenys	ENSNLEG00000000926	1 retrocopy	retro_nleu_1826,
Otolemur garnettii	ENSOGAG00000015569	1 retrocopy	retro_ogar_2846 ,