RetrogeneDB ID: retro_mmul_1579

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:30147938..30148858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.11028
• Ensembl ID: ENSMMUG00000013514
• Aliases: None
• Description: None

Sequence

>retro_mmul_1579
GAGAATGTATTCACCCGGCGATCAAAGATCTATTCCTACATGAGCCCCAACAGATGCTCTGGAATACGTTCCCCGCTTCC
GGAAGAGAACTCAGTTACACATCACGGAGTCAAATGCCAAGGAAACCGTTAGCCAGAATCTCCAAGAAACGAGAAGAGAA
AGGAAATGCAATACGGAGCACCAGGAAGTCTCAGGAACAGAAGATCAAACATGCCAGGAGAAGTCCCCTGGCACCTTTTC
CAAACCAATAATCTGAAGCAGCAGAACCTCCCAAAACTGTAACCTCGTCTTGTGATTCCACCAATGCAGCCATCACCAAG
CAAGCTCCGAAGAAGCCCTTCAAGGGCACACAGCACCCCCCGCCGCCCCCTCTGGAAAAAACATCAAGGAAAAACGCAAC
AGACTGGCAAACTCTCAGGTTTCTACCCTGTCCGAAGCAGCTCCAGGAAGAGCAAAGGTGAGCTGCAGTCCGAAGAAAGG
AAAATACCAGATGATTTGATTGAAGATGGGAAGAAAGAAGGAATGAAGAATGACCTCATTGATGGCAAAGGCAGGGATGC
CATCGCCATCAAGCATTTCTCCCAGAGTGCCTTTGTGGTGAAATAACCGCGGGGCTTCATCAAGATCGCGACGCCAAGAT
GCAGGAGGCTGTGTACGCACAGGACCCTCCGGAAGCTGTTACCTCTACTGTTTTCAGTATCTGAGCAAAACCTGCTGGAT
GCAACTAGAGACACAAATCGCTTAGGAAGACTGATCAATCACAGCAAATGTGGGAATTGCTAAACCAAACTGCAGGACAT
CGACGGCTACCTCACGGCCATCCTCAACACCTCCCGAGATAGTGAGGCCTGGGAGGTGCTCCTGTATTACTGTGGGGACC
GCAGCAAGGCTCCCTGGAAGCCGACGGGTGCCTGAAGCAT

Alignment

ORF - retro_mmul_1579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ENVFTGQSKIYSYMSPNKCSGMRFPLQEENSVTHHEVKCQG-KPLAGIYRKREEKRNAGNAVRSAMKSEE
          ENVFT..SKIYSYMSPN.CSG.R.PL.EENSVTHH.VKCQG.KPLA.I..KREEK...GNA.RS..KS.E
Retrocopy ENVFTRRSKIYSYMSPNRCSGIRSPLPEENSVTHHGVKCQG<KPLARISKKREEK---GNAIRSTRKSQE

Parental  QKIKDARRGPLAPFPNQKSEAAEPPKTPPSSCDSTNAAITKQALKK-PIKGKQAPR----KKAQGKTQQN
          QKIK.ARR.PLAPFPNQ.SEAAEPPKT..SSCDSTNAAITKQA.KK.P......PR....KK.QGKTQQ.
Retrocopy QKIKHARRSPLAPFPNQ*SEAAEPPKTVTSSCDSTNAAITKQAPKK>PSRAHSTPRRPLWKKHQGKTQQT

Parental  RKLTDFYPVRRSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGD
          .KL..FYPVR.SSRKSK.ELQSEERK..D.LIE.GK.EGMK.DLIDGKGR..IA.K.FS...FVV.....
Retrocopy GKLSGFYPVRSSSRKSKGELQSEERKIPDDLIEDGKKEGMKNDLIDGKGRDAIAIKHFSQSAFVVK*PRG

Parental  LIEIT-DAKKREALYAQD-PSTGCYMYYFQYLSKTYC-VDATRETNRLGRLINHSKCGNCQTKLHDIDGV
          .I.I..DAK..EA.YAQD.PS..CY.Y.FQYLSKT.C..DATR.TNRLGRLINHSKCGNC.TKL.DIDG.
Retrocopy FIKIA<DAKMQEAVYAQD<PSGSCYLYCFQYLSKT-C<LDATRDTNRLGRLINHSKCGNC*TKLQDIDGY

Parental  PHLILIASRDIAAGEELLYDYGDRSKA-SIEAHPWLKH
          ...IL..SRD..A.E.LLY..GDRSKA.S.EA...LKH
Retrocopy LTAILNTSRDSEAWEVLLYYCGDRSKA<SLEADGCLKH

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	14.34 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	14.68 RPM
SRP007412_cerebellum	0.00 RPM	14.08 RPM
SRP007412_heart	0.06 RPM	11.48 RPM
SRP007412_kidney	0.00 RPM	9.15 RPM
SRP007412_liver	0.00 RPM	3.80 RPM
SRP007412_testis	0.34 RPM	6.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1579 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1579 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1347

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294, retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579 ,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,