RetrogeneDB ID: retro_mmul_2216

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:32325039..32326224(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFT80
• Ensembl ID: ENSMMUG00000017282
• Aliases: None
• Description: None

Sequence

>retro_mmul_2216
ATTAAAGCATCTTTGAACTCTGCACACTTAGTTGTTTCAATGTCTCTTCAATGTTATGTGGTCTCCACAAAGAACTGGAA
TACACCAATTTTATTTGATCTCAAAGAAGGAACTGTTAGTTTAATCCTGCAGGCAGAAAGACATTTTCTTCTTGTAGATG
TTAGTAGTATCGATTTATATTCATATGAAGGGCACTTTATTTCATCTCCAGAATTTCCTGGAGTGAGAACAGATATTCTG
AATGCACAGACTGTGTCTCTGAGTAATGATATCATAGCAATGACACAAAGCTGATGAAGAAAAATAATCTTTTTTTTGAG
GCATCAACTGGAAAACCATTAGATGATGGAAAGTTTCTTCCTTGTAAAAATGAAATCTTGAAAGTTGCTCTGGATCAGAA
AGGACTTACCAATGATAGAAAAGTCACTTTTATTGATAAAAATAGAGATATCTATATCACCTCTGTGAAACAATTTGAGA
AGGAAGAAAAAAATTCTCAAACTTGAAACAATAGTGCATACTTTGGCATGGAATGATACAAGCACCGTCCTTTGCAGACT
TCAAGATACTCAATTTACAGTGTGGTATTATTCCTATATGGTTTATGCGGACAGTGACATTTTGCCTAAAACATTACATG
AAAGGGATACAAGTGAATTCAGTAAAAATTCCCATATTGTGAGTTTTGTTGGAAATCAGGTAACTATAGCAAGAGTTAAT
GGCCTTCTGGTTCACATCAGTGTATAACTATATCCTGTTATTCCCCCTAAATATGTAGGCAGTTCAAAATGGGAAGATGA
TTAAGACTTTGCCACTTTGTTGAGGACCAAACCATGTGAGCTTGTCTAGCTGCTATGGCAGTTGCTAATCAAGATATGAC
TATTACAGAAATAGACTATGCAGCAACTGGTGAAACTGATAAGGTTCAGTACTTCAATTCTATACAAAGTCTTCCATTTA
AATAATCAAAAATGGCCAACATAACTAAGGTTTAATGGGAACATACAGGAGGCTGAAATAGCATTTCTTCAGGCTGGCCT
CGTTTATGAAGCAATCCAGATCAATATTAATCTCTACAACTGAGAAAGGGCACTAGAATTGGCTGTAAAATACAAAACAC
ATGTTGATACAGTTCTTGCTTACTGTCAAAAGTTTTTGGAGACATTTGGTAAAGAAGAAACAAAC

Alignment

ORF - retro_mmul_2216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.25 %
• Parental protein coverage: 50.77 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKASLNYAHLVVSTSLQCYVFSTKNWNTPIIFDLKEGTVSLILQAERHFLLVDGSSIYLYSYEGRFISSP
          IKASLN.AHLVVS.SLQCYV.STKNWNTPI.FDLKEGTVSLILQAERHFLLVD.SSI.LYSYEG.FISSP
Retrocopy IKASLNSAHLVVSMSLQCYVVSTKNWNTPILFDLKEGTVSLILQAERHFLLVDVSSIDLYSYEGHFISSP

Parental  KFPGMRTDILNAQTVSLSNDTIAIRDKADEKII-FLFEASTGKPLGDGKFLSHKNEILEIALDQKGLTND
          .FPG.RTDILNAQTVSLSND.IA.......KII....EASTGKPL.DGKFL..KNEIL..ALDQKGLTND
Retrocopy EFPGVRTDILNAQTVSLSNDIIAMTQS**RKII<XXXEASTGKPLDDGKFLPCKNEILKVALDQKGLTND

Parental  RKIAFIDKNRDLCITSVKRFGKEE-QIIKLGTMVHTLAWNDTCNILCGLQDTRFIVWYYPNTVYVDRDIL
          RK..FIDKNRD..ITSVK.F.KEE..I.KL.T.VHTLAWNDT...LC.LQDT.F.VWYY...VY.D.DIL
Retrocopy RKVTFIDKNRDIYITSVKQFEKEE>KILKLETIVHTLAWNDTSTVLCRLQDTQFTVWYYSYMVYADSDIL

Parental  PKTLYERDASEFSKNPHIVSFVGNQVTIRRADGSLVHISISPYPAILHEYVSSSKWEDA-VRLCRFVKEQ
          PKTL.ERD.SEFSKN.HIVSFVGNQVTI.R..G.LVHIS...YP.I...YV.SSKWED...RLC.FV..Q
Retrocopy PKTLHERDTSEFSKNSHIVSFVGNQVTIARVNGLLVHISV*LYPVIPPKYVGSSKWEDD<LRLCHFVEDQ

Parental  TMWACLAAMAVANRDMTTAEIAYAAIGEIDKVQYINSIKSLPSKESKMAHI-LLFSGNIQEAEIVLLQAG
          TM.ACLAAMAVAN.DMT..EI.YAA.GE.DKVQY.NSI.SLP.K.SKMA.I.L.F.GNIQEAEI..LQAG
Retrocopy TM*ACLAAMAVANQDMTITEIDYAATGETDKVQYFNSIQSLPFK*SKMANI>LRFNGNIQEAEIAFLQAG

Parental  LVYQAIQININLYNWERLLDLREREKKRVKEDVMSYAKSYFETFGKQETN
          LVY.AIQININLYN.ER.L.L....K..V...V..Y.....ETFGK.ETN
Retrocopy LVYEAIQININLYN*ERALELAVKYKTHV-DTVLAYCQKFLETFGKEETN

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	1.23 RPM	21.74 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	12.53 RPM
SRP007412_cerebellum	1.03 RPM	11.11 RPM
SRP007412_heart	0.12 RPM	2.53 RPM
SRP007412_kidney	0.23 RPM	10.68 RPM
SRP007412_liver	0.08 RPM	0.67 RPM
SRP007412_testis	0.75 RPM	43.88 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2216 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000068885	1 retrocopy	retro_hsap_1568,
Macaca mulatta	ENSMMUG00000017282	1 retrocopy	retro_mmul_2216 ,
Pongo abelii	ENSPPYG00000014255	1 retrocopy	retro_pabe_1294,
Pan troglodytes	ENSPTRG00000015578	2 retrocopies	retro_ptro_1055, retro_ptro_2951,