RetrogeneDB ID: retro_mmul_2348

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:69609059..69611028(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF3
• Ensembl ID: ENSMMUG00000016301
• Aliases: None
• Description: None

Sequence

>retro_mmul_2348
AAGACAGTGAAGAGCGTGCTGGGTTTCTCAGAGCCTACAGTGGTCACAGCAGCATTGAACTGTGTGGGGAAGAGCATGGA
CAAGAAGAAGGCAGCCGATCATCTGATACCTTTTCTTGATGATTCTACTCTCCGATTTGTGGACAAACTGAGGCTGTAGG
AGAAAGGCGGAAGCTCTAGGCATTCCAAGTCTAGCAGTGACTGAAGCAGAAAACGAGAGCTAAAGAAGGTGTTTGGTGAT
GACTCTTGAGATCTCTAAGGAATCATCAGGAGTAAAGAAGCAGCGAATACCCCGTTTTGAGGAGGTGGAAGAAGAGCCTG
AGGTGATCCCTGGGCCTCCATCAGAGAGTCCTGGCATGCTGACTAAGCTCCAGATCAAACAGATGATGGACGCAGCAAAA
TGACATATGGAGGAGAGGAAAAAACAGCTACGCTTTATTAGCCCCCCTACACCTCAGCCAAAGACGCCTTCTTCCTCCCA
ACCAGAGCTACTTCCAATCGGCCACACTATTCTGCCTTCCCAGGCTGCCACTTTCATGAATGATGCCATTGAGAAGGCAA
GGAAAGCAGCTGAACTACAAGCTCGAATCCAAGCCCGGGTGGCACTGAAGCCAGGACTCATCAGCAATGCCAACATGCTG
GGCCTGGCTAATCTCCATGCCATGGGCATTGCTCCCCCAAAGGTGGAGTTAAATGACCAAATTAAACCTACACCACTGAT
CCTAGATGATCAAGGGTGCACTGTAGATGCAACATGCAAGGAGATTGAGCTGACACACTGCATGCCTACTCCTGCCAATA
TTCGTGCTGTGAAGAGGGAACCATTCAAGCATCAGCTAAAAGAAAAACCATCAGAAGACATGGAGTCCAATATCTTTTTT
GACCCTGAGTCTCCACTGTCGCTTCCCAGCGCCAGAAACGCACTTTTAAATTCCATGACAAGGGCAAATTTGAGAAGATT
GCTCAGCAATTAAGAACAAAGGCTCAACTGGAGAAGCTTCAGGCAGAGATTTCACAAGCAGCTCAAAAAATAGGCATCCA
TACTTTGACTAGGCTTGCCTTCATTGCTCCTAGGAAGGAGCTAAAGGAAGTAGATATCCCTGAAATTGAGTGGTGGGACT
CATATAATCCCCAATGGCTTTGACCTTACAGAGGAAAATCCCAAGAGAGAAGATTATTTTGGAATCACAAATCTTGTTGA
ACATCCAGCCCAGCTCAATCCTCCAGTCGACAATGACACACCAGTTACTCTGGGAGTGTATCTTACCAAGAAGGAACAGA
AAAAACTTCAGAGACAGACAAGGAGGGAAGCACAGAAGGAACTACTAGAAAAAGTCAGGCTGGGCCTGATGCCTCCTCCA
GAACCCAAAGTGAGAATTCTAATTTGACGCAAGTATTAGGAACAGAAGCTGTTCAAGACTACACGAAGGTAGAAGTCCAT
GTCAGAGCTCAGATGGCAAAAAGACAGAAAGTGCATGAAGAGGTCAATTCTGCCTGAAAACTCACAGCAGAATAGAGAAA
GGTCAAGAAAATTTAAAAGCTTAAGACATTTCACAGGGGTACACATATCTGTATATGGAGTTACAAATTTGAGCACCCCA
GCCAAGAAGTTCAAGATTGAGGCCACTGCTGGGCAACTGTACCTGACGGGGTGGTGGTACTGCACAAGGATGTCAACGTG
GTAGTAGTGGAAGGGGGCCCCAAGGCCCAGAAGAAATGTAAGCATCTTAATGCTGCATCGGATAAAGTGGGATGAATGGA
CATCTAACACAAAGGGAGATGATCATGAGGAATCTAATGAGGAAGCTGTGAAGAAAACCAACAAATGTATACTATTCTGG
GAGGGTACAGCCAAAGACCAGAGCTTTGGAGAGATGAAGTTTAAACAGTGTCCTACAGAGAACATAGCTTGTGAGCATTT
CAGAAAGCATGGGGCTGAACATTACTGGAACCTTGCCCTAAGTGAATCT

Alignment

ORF - retro_mmul_2348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 96.78 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  KTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTLRFVDKLFEAVEEGRSSRHSKSSSDRS
          KTVK.VLGFSEPTVVTAALNCVGK.MDKKKAADHL.PFLDDSTLRFVDKL....E.G.SSRHSKSSSD.S
Retrocopy KTVKSVLGFSEPTVVTAALNCVGKSMDKKKAADHLIPFLDDSTLRFVDKL-RL*EKGGSSRHSKSSSD*S

Parental  RKRELKEVFGDDS-EISKESSGVKKRRIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMMEAATRQIEE
          RKRELK.VFGDDS.EISKESSGVKK.RIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMM.AA....EE
Retrocopy RKRELKKVFGDDS>EISKESSGVKKQRIPRFEEVEEEPEVIPGPPSESPGMLTKLQIKQMMDAAK*HMEE

Parental  RKKQLSFISPPTPQPKTPSSSQPERLPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLIG
          RKKQL.FISPPTPQPKTPSSSQPE.LPIG.TI.PSQAATFMNDAIEKARKAAELQARIQA..ALKPGLI.
Retrocopy RKKQLRFISPPTPQPKTPSSSQPELLPIGHTILPSQAATFMNDAIEKARKAAELQARIQARVALKPGLIS

Parental  NANMVGLANLHAMGIAPPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVKREQFKQ
          NANM.GLANLHAMGIAPPKVEL.DQ.KPTPLILD.QG.TVDAT.KEIELTH.MPT..ANIRAVKRE.FK.
Retrocopy NANMLGLANLHAMGIAPPKVELNDQIKPTPLILDDQGCTVDATCKEIELTHCMPT-PANIRAVKREPFKH

Parental  QLKEKPSEDMESNTFFDPR-VSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKLQAEISQAARKTGI
          QLKEKPSEDMESN.FFDP..VS...SQRQ.RTFKFHDKGKFEKIAQ.LRTKAQLEKLQAEISQAA.K.GI
Retrocopy QLKEKPSEDMESNIFFDPE<VSTVASQRQKRTFKFHDKGKFEKIAQQLRTKAQLEKLQAEISQAAQKIGI

Parental  HTSTRLALIAPKKELKEGDIPEIEWWDSYI-IPNGFDLTEENPKRE-DYFGITNLVEHPAQLNPPVDNDT
          HT.TRLA.IAP.KELKE.DIPEIEWWDSY...P....L....P....DYFGITNLVEHPAQLNPPVDNDT
Retrocopy HTLTRLAFIAPRKELKEVDIPEIEWWDSYN<SPMALTLQRKIPREK<DYFGITNLVEHPAQLNPPVDNDT

Parental  PVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRI-SNLMRVLGTEAVQDPTKVEAHVR
          PVTLGVYLTKKEQKKL.RQTRREAQKEL.EKVRLGLMPPPEPKVRI.SNL..VLGTEAVQD.TKVE.HVR
Retrocopy PVTLGVYLTKKEQKKLQRQTRREAQKELLEKVRLGLMPPPEPKVRI<SNLTQVLGTEAVQDYTKVEVHVR

Parental  AQMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQGVHISVYRVRNLSNP-AKKFKIEANAGQLYLT
          AQMAKRQK.HEE.N.A.KLTAE.RKVKKI.KLK.....G.HI..........P.AKKFKIEA.AGQLYLT
Retrocopy AQMAKRQKVHEEVNSA*KLTAE*RKVKKI*KLK-TFHRGTHICIWSYK-FEHP>AKKFKIEATAGQLYLT

Parental  -GVVVLHKDVNVVVVEGGPKAQKKFKR-LMLHRIKWDEQTSNTKGDDDEESDEEAVKKTNKCVLVWEGTA
          .GVVVLHKDVNVVVVEGGPKAQKK.K..LMLHRIKWDE.TSNTKGDD.EES.EEAVKKTNKC.L.WEGTA
Retrocopy <GVVVLHKDVNVVVVEGGPKAQKKCKH>LMLHRIKWDEWTSNTKGDDHEESNEEAVKKTNKCILFWEGTA

Parental  KDRSFGEMKFKQCPTENMAREHFKKHGAEHYWDLALSES
          KD.SFGEMKFKQCPTEN.A.EHF.KHGAEHYW.LALSES
Retrocopy KDQSFGEMKFKQCPTENIACEHFRKHGAEHYWNLALSES

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	21.96 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	15.87 RPM
SRP007412_cerebellum	0.06 RPM	33.45 RPM
SRP007412_heart	0.00 RPM	20.67 RPM
SRP007412_kidney	0.23 RPM	21.71 RPM
SRP007412_liver	0.00 RPM	8.51 RPM
SRP007412_testis	1.36 RPM	63.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2348 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2348 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4069
Pan troglodytes	retro_ptro_2758
Callithrix jacchus	retro_cjac_1499

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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,