RetrogeneDB ID: retro_ogar_3052

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873705.1:274432..276478(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF3
• Ensembl ID: ENSOGAG00000005352
• Aliases: None
• Description: pre-mRNA processing factor 3 [Source:HGNC Symbol;Acc:17348]

Sequence

>retro_ogar_3052
ATGGCACTGTCTAAGAAGGAGCTGGATGAGCTGAAACCATGGATAGAGAAGATAGTGAAGAGAGTATTGGATTTCTCAGA
GCCCACAGTGGTAACAGCAATACTGAACTGTGTGGGAAAGGGCATGGACAAGAAGACAGCTGACCATCTGAAATCTTTTC
TTGATGACTCTACTCTCCGATTTGTGGACAAACTATTTGAGGCTGTGTTAGAGGGCCGAAGCTCTAGGCATTCCAAGTCT
AGCAGTGAAAGGAGCAGAAAATGTGCACTAAAGAAGGTGTTTGGTGATGACTCTGAGATTGCCAAAGAATCTTCGGGAGT
AAAGAAGTGATGAATACTCCATTTTGAGGAGGTAGAAAAAGGGCCAGAGGTAATCCCTGGTCCTCCATCAGAGAGTCCGG
GCATGCTAACTAAACTCTAGATCAAACAGATGATGGAAGCAGCACCACGACAAATTGAGGAGAGAAAATAACAATTGAGC
TTCATTAGCCCTCCTACACCTCAGCCAAAGACTCCTTCTTCCTCTCAACCAGAGTGACTTCCAATTGGCAACACTATTCA
GCCCTCCAAGGCTGCCACTTTCATGAATGATGCCATTGAGAAAGCAAGGAAAGCAGCTGAACTACAAGCTAGAATCCAAG
CCCAGCTGGCACTGAAGCCAGGACTCATTGGCAATGCCAACATGGTGGGCCTGGCTAATCTCCATGCTATGGGCATTGCT
CCCCTGAAAGTGGAGTTAAAAGATGAAACTAAACCTACACCACTGATCCTAGATGAACAGGGTCACACTGTAGATGCAAC
AGGCAAGGAGATTGAGCTGACATATCGCATGCCTACTTTTAAGGCCAATATTCGTGCTGTGAAAAGGGAACAATTCAAGC
AACAGCTAAAAGAAAAGCCATCAGAAGATATGGAGTCCAATATGGTTTTTGACCCCCGAGTTTCAATTGCCCCTTCCCAA
CGCCAGAGACAAACTTTTAAATTCCATGACAAAGGCAAATTTGAGAAGATTGCTTAGTGATTACAGACCAAGGCTCAACT
GGAGAAGCTGCAGACAGAGATCTCACAGGCAGCTTGAAAAACAGGCATCCATACTTCCTCTAGGCTTGCTCTCATTGCTC
CTAAAAAGAAATTAAAGGAAGGAGATATACCTGAAGTTGAGTGGTGGGACTCTTACATCATCCCCAAAGGCTTTGACCTT
ACAGAGGAAAATTCCAAGAGAGAAGATTATTTTGGAATCACAAATCTTGTTGAACATCCAGCCAAGCCTAATCCTCCAGT
GGACAATGACACACCAGTTACTCTGGGGGTGTATCTTACCAAGAAGGAACAGAAGAAACTTCGGAGGCAGACAAGGAGAG
AAGCACAGAAAGAACTACAAGAGAAAGTCAGGCTGGGCCTAATGCCTCCCCTAGAACCCAAAGTGAGAATTTCTAATCTG
ATGCAAGTATTAGGCACAGAAGCTGTTCCAGAGCCCACGAAGGTAGAAGCCCATGTCAAAGCTCAAATGGCAAAAAGACA
GAAAGCGCATGAAGAGGCCAACGCTGCCCGAAAACTTATAGCAGAACAGAGAAAGGTCAAGAAAATTAAAAAGCTTAAAG
AAGGCATTTCACAGGGGGTACACATATCTGTATATAGAGTTTGAAATTTGAGCAACCCAGCCAAGAAGTTCAAGATTAAG
GCCAATGCTGGGCAACTGTACCTGACAGAGGTGGTGGTACTGCACAAGGATGTCAACGTGGTAGTAGTGGAAGGGGGCCC
CAAAGCCCAGAAGAAATTTAAGCGTCTTATGCTGCTTCAGATAAAGTGGGACGAACAGACATCTAACACAAAGGGAGATG
ATGATGAGGAATCTGATGAGGAAGCTGTGAAGAAAACCAACAAATGTATACAAGTCTGAGAGGGTACAGCCAAAAACCGG
AGCTTTTGAGAGATGAAGTTCAAACAGTGCCCTACAGAGAACATGGCTCGTGACCATTTCAAAAATCATGGGGCTGAACA
CTACTGGGACTTTGCACTGAGTGAATCTGTGTTAGAGTCCACTGAC

Alignment

ORF - retro_ogar_3052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 11
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAV
          MALSK.ELDELKPWIEK.VKRVL.FSEPTVVTA.LNCVGKGMDKK..ADHLK.FLDDSTLRFVDKLFEAV
Retrocopy MALSKKELDELKPWIEKIVKRVLDFSEPTVVTAILNCVGKGMDKK-TADHLKSFLDDSTLRFVDKLFEAV

Parental  EEGRSSRHSKSSSDRSRKRELKEVFGDDSEIAKESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKL
          .EGRSSRHSKSSS.RSRK..LK.VFGDDSEIAKESSGVKK..I..FEEVE..PEVIPGPPSESPGMLTKL
Retrocopy LEGRSSRHSKSSSERSRKCALKKVFGDDSEIAKESSGVKK**ILHFEEVEKGPEVIPGPPSESPGMLTKL

Parental  QIKQMMEAATRQIEERKKQLSFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQ
          .IKQMMEAA.RQIEERK.QLSFISPPTPQPKTPSSSQPE.LPIGNTIQPS.AATFMNDAIEKARKAAELQ
Retrocopy *IKQMMEAAPRQIEERK*QLSFISPPTPQPKTPSSSQPE*LPIGNTIQPSKAATFMNDAIEKARKAAELQ

Parental  ARIQAQLALKPGLIGNANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPT
          ARIQAQLALKPGLIGNANMVGLANLHAMGIAP.KVELKD.TKPTPLILDEQG.TVDATGKEIELT.RMPT
Retrocopy ARIQAQLALKPGLIGNANMVGLANLHAMGIAPLKVELKDETKPTPLILDEQGHTVDATGKEIELTYRMPT

Parental  LKANIRAVKREQFKQQLKEKPSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAHNHK
          .KANIRAVKREQFKQQLKEKPSEDMESN..FDPRVSIAPSQRQR.TFKFHDKGKFEKIA..L.TKA...K
Retrocopy FKANIRAVKREQFKQQLKEKPSEDMESNMVFDPRVSIAPSQRQRQTFKFHDKGKFEKIA**LQTKAQLEK

Parental  MEAELAQASRDGAIHPGTYWYLIPIKFVSIE--IIENDWVQTWPWPNGNFSTEENPKREDYFGITNLVEH
          ...E..QA.....IH......LI..K....E..I.E..W......P.G...TEEN.KREDYFGITNLVEH
Retrocopy LQTEISQAA*KTGIHTSSRLALIAPKKKLKEGDIPEVEWWDSYIIPKGFDLTEENSKREDYFGITNLVEH

Parental  PAQLNPPATNXDTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRISNLMRVLGTEA
          PA..NPP..N.DTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPP.EPKVRISNLM.VLGTEA
Retrocopy PAKPNPPVDN-DTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPLEPKVRISNLMQVLGTEA

Parental  VQDPTKVEAHVKAQMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQGVHISVYRVRNLSNPAKKFK
          V..PTKVEAHVKAQMAKRQKAHEEANAARKL.AEQRKVKKIKKLKE.ISQGVHISVYRV.NLSNPAKKFK
Retrocopy VPEPTKVEAHVKAQMAKRQKAHEEANAARKLIAEQRKVKKIKKLKEGISQGVHISVYRV*NLSNPAKKFK

Parental  IEANAGQLYLTGVVVLHKDVNVVVVEGGPKAQKKFKRLMLHRIKWDEQTSNTKGDDDEESDEEAVKKTNK
          I.ANAGQLYLT.VVVLHKDVNVVVVEGGPKAQKKFKRLML..IKWDEQTSNTKGDDDEESDEEAVKKTNK
Retrocopy IKANAGQLYLTEVVVLHKDVNVVVVEGGPKAQKKFKRLMLLQIKWDEQTSNTKGDDDEESDEEAVKKTNK

Parental  CVLVWEGTAKDRSFGEMKFKQCPTENMAREHFKKHGAEHYWDLALSESVLESTD
          C..V.EGTAK.RSF.EMKFKQCPTENMAR.HFK.HGAEHYWD.ALSESVLESTD
Retrocopy CIQV*EGTAKNRSF*EMKFKQCPTENMARDHFKNHGAEHYWDFALSESVLESTD

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_3052 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009926	1 retrocopy	retro_cjac_1499,
Macaca mulatta	ENSMMUG00000016301	1 retrocopy	retro_mmul_2348,
Nomascus leucogenys	ENSNLEG00000009841	1 retrocopy	retro_nleu_2529,
Otolemur garnettii	ENSOGAG00000005352	4 retrocopies	retro_ogar_2360, retro_ogar_3052 , retro_ogar_374, retro_ogar_409,
Pan troglodytes	ENSPTRG00000001254	1 retrocopy	retro_ptro_2758,