RetrogeneDB ID: retro_ogar_374

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873520.1:14384556..14385622(-)
• 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_374
CTGAAAAATGGCTCTAAGAGGGAGCTGGATGAGCTGAAACCATGGATGGAGAAGACAGTGGTCACAGCAGCTCTGAACTG
TTTGGGGAAAAGCGTGGACAAGGAGAAGGCAGCCGGCCATCTGAAACCTTTTCTTGATGATTCTACTCTCCGATTTGTGG
ACAAACTATTTGAGGCTGTGGAGGAGGACCGAAGCGTTAGGCATTCCAAGTCTATCAGTGATAGGAGCAGAAAACAAGAG
CTAAAGGAGTTGTTTGGTGATGACTCTGAGATTTCCAAAGAATCTTCGGGAATGAAGAAGCAAGGAATACCTGGTTTTGG
GGAGGCGGAAGAAGAGTCAGAGGTGATCCCTGGTCCTCCATCGGAGAGCCCGGGAATGCTGTCTAAGCTTCAGACCAAAT
AGATGATAGAAACAGCAACAAGACAAGTTGAAGAGAGAAAAAAACAACTGAGCTTCATTTGCGCCCCCTATACCTCAGCC
AAAGATTCCTTCTTTCTCCCATCCAGAGCGACTTCCAATTGGCAACACCATTCAGCCCTCCCAGGCTGCCACTTTCATGA
ATGATGCCATTGAGAAAGCAAAGAAAGCAGCTGAACTACAAGCTTGAATCCAAGCCCAGCTGGCACTGAAGCCAGGACTT
GTTGGCAATGCCAACATGGTGGGCCTGGCTAATCTCCATGCTATGGGCATTGCTCCCTTGAAGGTGGAGTCAAAAGATCA
AACTAAATCTACACCATTGATCCTAGATGAACAGGGTCACACTGTAGATGCAACAGGCAAGGAGATTGAGCTGACACATT
GCATGCCTACTCTTAAGGCCAATATTGGTGCTGTGAAAAGGGAAAAATTCAAGCAACAGCTAAAAGAAAAGCCATCAGAA
GATATGGAGTCCAATATGTTTTTTGACCCCCTGAGTTTCAACTGCCCCTTCCCAGCTCCAGAGATGAACTTTTAAATTCC
ATGACAAAGGAAATTTGAGAAGATTGCTCAGCGATTACGGACCAAGGCTCAACTGGAGAAGCTGCAGGCAGAGGTCTCAC
AAGCAGCTCAAAAAATAGGCATCTAC

Alignment

ORF - retro_ogar_374 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.05 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAVEEGRSSRHSK
          LK..............E.TVVTAALNC.GK..DK.KAA.HLKPFLDDSTLRFVDKLFEAVEE.RS.RHSK
Retrocopy LKNGSKRELDELKPWMEKTVVTAALNCLGKSVDKEKAAGHLKPFLDDSTLRFVDKLFEAVEEDRSVRHSK

Parental  SSSDRSRKRELKEVFGDDSEIAKESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMMEAAT
          S.SDRSRK.ELKE.FGDDSEI.KESSG.KK..IP.F.E.EEE.EVIPGPPSESPGML.KLQ.K.M.E.AT
Retrocopy SISDRSRKQELKELFGDDSEISKESSGMKKQGIPGFGEAEEESEVIPGPPSESPGMLSKLQTK*MIETAT

Parental  RQIEERKKQLSFI-SPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLAL
          RQ.EERKKQLSFI..PP.PQPK.PS.S.PERLPIGNTIQPSQAATFMNDAIEKA.KAAELQA.IQAQLAL
Retrocopy RQVEERKKQLSFI>APPIPQPKIPSFSHPERLPIGNTIQPSQAATFMNDAIEKAKKAAELQA*IQAQLAL

Parental  KPGLIGNANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVK
          KPGL.GNANMVGLANLHAMGIAP.KVE.KDQTK.TPLILDEQG.TVDATGKEIELTH.MPTLKANI.AVK
Retrocopy KPGLVGNANMVGLANLHAMGIAPLKVESKDQTKSTPLILDEQGHTVDATGKEIELTHCMPTLKANIGAVK

Parental  REQFKQQLKEKPSEDMESNTFFDPR-VSIAPSQRQRRTFKFHDKG-KFEKIAQRLRTKAHNHKMEAELAQ
          RE.FKQQLKEKPSEDMESN.FFDP..VS.APSQ.QR.TFKFHDKG.KFEKIAQRLRTKA...K..AE..Q
Retrocopy REKFKQQLKEKPSEDMESNMFFDPL>VSTAPSQLQR*TFKFHDKG<KFEKIAQRLRTKAQLEKLQAEVSQ

Parental  ASRDGAIH
          A.....I.
Retrocopy AAQKIGIY

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_374 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,