RetrogeneDB ID: retro_ogar_409

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873521.1:8352899..8354944(+)
• 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_409
ATGACACTGTCTAAGAGGGAGCTGGATGAACTGAAACCATGGATAGAGACCATAGTGAAGAGAGTATTGGGTTTCTCAGA
GCCCACAGTGGTAACAGCAGCACTGAACTGTGTGGGGAAGGGCATGGACAAGAAAAAGGCAGTCGACCATCTGAAACCTT
TTCTTGATGATTCTACTCTCCAATTTGTGGACAAACTATTTGAGGCTGTGGAGGAAGGCCAAAGCTCTAGGTATTCCAAG
TCCAGCAGTGATAGGAGCAGAAAACAAGAGCTAAAGGAGTGTTTGGTGATGACTCTGAGGTTTTCAAAGAATCTTCGGGA
GTAAAGAAGCAATGAATACCCCATTTTGAGGAGGTGGAAGAAGAGCCAGAAGTGATCCCTGGTCCTCCATCAGAGAGCCC
GGGCATGCTGACTAAGCTTTAGATCAAACAGATGATGGAAGCAGCGACACAACAAATTGAGGAGAGAAAAAAACAACTGA
GCTTCGTTAGTCCCCATACACCGCAGCCGAAGACTCCTTCTTCCTCCCAACCAGAGCGACTTCCAATTGGCAACACTATT
CAGCCCTCCCAGGCTGCCACTTTCATGAATAATGTCATTGAGAAGGCAAGGAAAGCAGCTGAACTACAAGCTCGAATCCA
AGCCCAGCTGGCACTGAAGCCAGAACTCACTGGCAACGCCAACATGGTGGGCCTGGCTAATCTCCATGCTATGGGCATTG
CTCCCCTGAAGGTGGATTTAAAAGACCAAACTAAACCTACACCACTGATCCTAGATGAGCAGAGTTGCACTGTAGATGCA
ACAGGCAAGGAGATTGAGCTGACACATCGCATGCCTACTCTTAAAGCCAATATTCATGCTGTGAAAAGGGCACAATTCAA
GCAACAGCTAAAAGAAAAGCCATCAGAAGATATGGAGTCCAATATGTTTTTTGACCTCCGAGTTTCAATTGCCCCTTCCC
ACCGCCAGAGATGAACTTTTAAATTCCATGACAAAGGCAAATTTGAGAAGATTGCTCAGTGATTACGGACCAAGGCTCAA
CTGGAGAAGCTGCAGGCAGAGATCTCACAAGCAGCTCAAAAAATGGGCATCCATACTTCCACTATGCTTGCCCTCATTAC
TCCTAAAAAGGAATTAAAGGAAGGCGATATCCTTGAAGTTGAGTGGTGGGACTCTTACGTCATCCCCAATGGCTTTGACC
TTACAGAGGAAAATCCCAAGAGAGAAGATTATTTTGGAATCACAAATCTTGTCGAACATCCAGCTCAGCTTAATCCTCCA
GTTAACAATGACACACCAGTTACTCTGGGGGTATATCTTACCAAGAAGGAACAGAAGAAACTTCGAAAGCAGACAAGGAG
AGAAGAGCAGAAAGAACTACAAGAGAAAGTCAGGCTGGGCTTGATGCCTCCTCCAGAACCCAAAGTGAGAATTTCTAATC
TGATGTGAGTATTAGGCACAGAAGCTGTTCAAGACCCCATGAAGGTAGAAGCCCATGTCAAAGCTCAAATGGCAAAAAGA
CAGAAAGCACATGAAGAGGCCAACACTGCCCGAAAACTTACAGCAGAACAGAGAAAGGTCAAGAAAATTAAAAAGCTTAA
AGAAGACATTTCACAGGGGGTACACATATCTGTATATAGAGTTTGAAATTTGAGCAACCCAGCCAAGAAGTTCAAGATTG
AGGCCAATGCTGGGCAACTGTACCTGACAGGGGTGGTGTTCCTGCACAAGGACGTCAACGTGGTAGTAGTAGAAAGGGGC
CCCAATGCCCAGAATAAATTTAAGCGTCTTATGCTGCATCGGATAAAGTGGGATGAACAGACATCTAACACGAAGGGAGA
TGATGATGAGGACTCTGATGAGAAAGCTGTGAAGAAAACCAACAAATGTGTACTAGTCTGGGAGGGTACAGCCAAAGACC
GGAGCTTTGGAGAGGTGAAGTTCAAACAGTGCCCTACAAAGAATGTGGCTCGTGAGCATTTCAAAAAGCATGGGGCTGAA
CACTACTGGGACCTTGTACTGAGGGAATCTGTGTTAGAGTCCACT

Alignment

ORF - retro_ogar_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.84 %
• Parental protein coverage: 99.85 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAV
          M.LSKRELDELKPWIE..VKRVLGFSEPTVVTAALNCVGKGMDKKKA.DHLKPFLDDSTL.FVDKLFEAV
Retrocopy MTLSKRELDELKPWIETIVKRVLGFSEPTVVTAALNCVGKGMDKKKAVDHLKPFLDDSTLQFVDKLFEAV

Parental  EEGRSSRHSKSSSDRSRKRELKE-VFGDDSEIAKESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTK
          EEG.SSR.SKSSSDRSRK.ELKE.VFGDDSE..KESSGVKK..IP.FEEVEEEPEVIPGPPSESPGMLTK
Retrocopy EEGQSSRYSKSSSDRSRKQELKE<VFGDDSEVFKESSGVKKQ*IPHFEEVEEEPEVIPGPPSESPGMLTK

Parental  LQIKQMMEAATRQIEERKKQLSFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAEL
          L.IKQMMEAAT.QIEERKKQLSF.SP.TPQPKTPSSSQPERLPIGNTIQPSQAATFMN..IEKARKAAEL
Retrocopy L*IKQMMEAATQQIEERKKQLSFVSPHTPQPKTPSSSQPERLPIGNTIQPSQAATFMNNVIEKARKAAEL

Parental  QARIQAQLALKPGLIGNANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMP
          QARIQAQLALKP.L.GNANMVGLANLHAMGIAP.KV.LKDQTKPTPLILDEQ..TVDATGKEIELTHRMP
Retrocopy QARIQAQLALKPELTGNANMVGLANLHAMGIAPLKVDLKDQTKPTPLILDEQSCTVDATGKEIELTHRMP

Parental  TLKANIRAVKREQFKQQLKEKPSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAHNH
          TLKANI.AVKR.QFKQQLKEKPSEDMESN.FFD.RVSIAPS.RQR.TFKFHDKGKFEKIAQ.LRTKA...
Retrocopy TLKANIHAVKRAQFKQQLKEKPSEDMESNMFFDLRVSIAPSHRQR*TFKFHDKGKFEKIAQ*LRTKAQLE

Parental  KMEAELAQASRDGAIHPGTYWYLIPIKFVSIE--IIENDWVQTWPWPNGNFSTEENPKREDYFGITNLVE
          K..AE..QA.....IH..T...LI..K....E..I.E..W......PNG...TEENPKREDYFGITNLVE
Retrocopy KLQAEISQAAQKMGIHTSTMLALITPKKELKEGDILEVEWWDSYVIPNGFDLTEENPKREDYFGITNLVE

Parental  HPAQLNPPATNXDTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRISNLMRVLGTE
          HPAQLNPP..N.DTPVTLGVYLTKKEQKKLR.QTRRE.QKELQEKVRLGLMPPPEPKVRISNLM.VLGTE
Retrocopy HPAQLNPPVNN-DTPVTLGVYLTKKEQKKLRKQTRREEQKELQEKVRLGLMPPPEPKVRISNLM*VLGTE

Parental  AVQDPTKVEAHVKAQMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQGVHISVYRVRNLSNPAKKF
          AVQDP.KVEAHVKAQMAKRQKAHEEAN.ARKLTAEQRKVKKIKKLKEDISQGVHISVYRV.NLSNPAKKF
Retrocopy AVQDPMKVEAHVKAQMAKRQKAHEEANTARKLTAEQRKVKKIKKLKEDISQGVHISVYRV*NLSNPAKKF

Parental  KIEANAGQLYLTGVVVLHKDVNVVVVEGGPKAQKKFKRLMLHRIKWDEQTSNTKGDDDEESDEEAVKKTN
          KIEANAGQLYLTGVV.LHKDVNVVVVE.GP.AQ.KFKRLMLHRIKWDEQTSNTKGDDDE.SDE.AVKKTN
Retrocopy KIEANAGQLYLTGVVFLHKDVNVVVVERGPNAQNKFKRLMLHRIKWDEQTSNTKGDDDEDSDEKAVKKTN

Parental  KCVLVWEGTAKDRSFGEMKFKQCPTENMAREHFKKHGAEHYWDLALSESVLEST
          KCVLVWEGTAKDRSFGE.KFKQCPT.N.AREHFKKHGAEHYWDL.L.ESVLEST
Retrocopy KCVLVWEGTAKDRSFGEVKFKQCPTKNVAREHFKKHGAEHYWDLVLRESVLEST

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_409 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,