RetrogeneDB ID: retro_mmul_2370

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:123167258..123169015(-)
• Located in intron of: ENSMMUG00000002607

Retrocopy information

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

Parental gene information

• Parental gene symbol: NCAPG
• Ensembl ID: ENSMMUG00000018070
• Aliases: None
• Description: None

Sequence

>retro_mmul_2370
CTGGCTATTTGACAGGAGATTCTTACTCTACCCACAACCCCAATATCCATGGTTCCTTTTCTTGTTGAAGGACTGCTGCA
CATTATTATAGATGATAATAAGAGAACAGAAATTATCTCAGAGATTGGGGTACCCATTATTACTGTTGGTGTTTATGATG
ACCCAGTTGATGCAAGAAAGAAAGGACTCAAGATGGCTGAAATAAAAGTTAAGTGTATTGAAGCCAAAGAAGCTTTGGAA
AATTATATTACCTTACAGGATTTTCACTTGGCATCAAAATTAAAAGAAGAAATAAAAGCATTAGAAGATGTCAAAAGAAA
CGTTTTGAAAGAGACAGAGCAATTTGAAATTAAAGAAGTCCACATAGAGAAGAATGACGCAGAAACATTATAGAATGTCT
TATGCTGTGAACTGTTGAAGCAGATGTCCATTTCAGCAGGCATAAGTGCAGCCATGAATGGGATCATTGAATTTTTTATT
CTTCCTAAGATAATACATGTTTACCCTAGAGTAAGAAATCTGGCTGTTTTACGCTCGGGAGCTGCAGACTACAGAATCAG
GATTTTGCATGTAACACTTTGTGTTATCATTGCAAGTTTTGCAAATTGATGATGTCACAATAAAAATAAGTGCTTTAAAG
GGAATCTTTGACTAGCTGATAATGTTTGGGGTTGAACCACTTAAACCTAAAAAATCAAAGCCTTTTAATATGAAGGTGCA
GAGATAAACAGTGATTGATGAGCAAGAGTCATAAAAAGTTGAAAAGGCCCTTACAGCGAAGAATGTTCTGAAACTCCTTT
CTGATTTCTTAGATAGTGAGGTATCTACACTTAGGACAGGAGCCATAGAAGGACTAGCCAAGCCGATGTTCTCTGGGCTT
TGGGTCAGCAGCAGGACTTTTTCCCATCTTATTTTGTAATGGTAGAGTCCTGTGACTGAAGAGGATGTTCGACTTCGACA
TTGCCTAGGCGTGTTCTCCCCCATGTTTGCTTATGCAAGCAGGACTGATCAGGAATGCTTTGAAGAAGTTTCTCTTCCAA
GCCTGCAAACACTGGCCAGTGCTCCTGCATCTTCTCCTTTAGCTGAAATTCATATCAGAAATGTTGTTGAGTTACTTATA
GATTTGATGAGAACAAGCAGATTAAATCCTCAGGCCAAGAATTCCTAAGATTATCAGGCCTTAACAGTACATGACAGTTT
GGCTATAAAAATTTGCCGTGAGATCTTAACAAGTCCATGCTCACCAGAAATGCGGGTCTCTATAAAAGCATTGAGTTCTT
TAGAACTCAATAGCCATCTTGCAAAAGATCTTCTGGTTCTATTGAATGGGATTCTGGAGCAAGTAAAGGATGGGGCACGT
CTGAAAGCTTTGGAGAAAATCAAGATTCAGTTGGCAAAAAGGAAATAAAGAATTTGGTGACCAGCCTGAAGCAGCACAGG
ATGCCAACTTGACTACAACTATTTTTCAAAATGAAGATGAAAAGAATAAGGAAGTACATATGACTCTTGTTAGGGATGTA
AAAGCAACCCTGGCATCAAAATCTAGTCAGCAAAAGACTAACAGGGGACAGAGAAAAGTGACAGCTTCAGCTAGGAAGAA
GAGGAGACATCAGATTGCTGAGGCTGACTCTGAAAGTGACCATGAAGTTCTAGAACCAGAATCAGAAATGAAGATGAAAC
TACCAAGACAAGCCAAAACAGCAGTGCTGGAAAAAAGTAAACCTAATCTGGCACAATTTCTCAATGAAGATTTAAGT

Alignment

ORF - retro_mmul_2370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.39 %
• Parental protein coverage: 58.73 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LAVLQEILILPTIPVSLVSCLVERLLHIIIDDNKRTQIVTEIISEIRAPIVTVGVNDDPADVRKKELKMA
          LA..QEIL.LPT.P.S.V..LVE.LLHIIIDDNKR....TEIISEI..PI.TVGV.DDP.D.RKK.LKMA
Retrocopy LAI*QEILTLPTTPISMVPFLVEGLLHIIIDDNKR----TEIISEIGVPIITVGVYDDPVDARKKGLKMA

Parental  EIKVKLIEAKEALENCITLQDFNRASELKEEIKALEDARINLLKETEQLEIKEVHIEKNDGETLQKCLIL
          EIKVK.IEAKEALEN.ITLQDF..AS.LKEEIKALED...N.LKETEQ.EIKEVHIEKND.ETL.....L
Retrocopy EIKVKCIEAKEALENYITLQDFHLASKLKEEIKALEDVKRNVLKETEQFEIKEVHIEKNDAETL*N--VL

Parental  CYELLKQMSISTGLSATMNGIIESLILPGIISVHPVVRNLAVL-CLGCCGLQNQDFASK-HFVLLLQVLQ
          C.ELLKQMSIS.G.SA.MNGIIE..ILP.II.V.P.VRNLAVL..LG.C.LQNQDFA...HFVL.LQVLQ
Retrocopy CCELLKQMSISAGISAAMNGIIEFFILPKIIHVYPRVRNLAVL<TLGSCRLQNQDFACN<HFVLSLQVLQ

Parental  IDDVTIKISALKAIFDQLMMFGIEPFKTKK-IKTLHCEGTEINSD-DEQESKEVEETATAKNVLKLLSDF
          IDDVTIKISALK.IFD.L.MFG.EP.K.KK.IK....EG.EINSD.DEQES..VE...TAKNVLKLLSDF
Retrocopy IDDVTIKISALKGIFD*LIMFGVEPLKPKK<IKAF*YEGAEINSD>DEQES*KVEKALTAKNVLKLLSDF

Parental  LDSEVSELRTGAAEGLAKLMFSGLLVSSRILSRLILLWYNPVTEEDVRLRHCLGVFFPIFAYASRTNQEC
          LDSEVS.LRTGA.EGLAK.MFSGL.VSSR..S.LIL.W..PVTEEDVRLRHCLGVF.P.FAYASRT.QEC
Retrocopy LDSEVSTLRTGAIEGLAKPMFSGLWVSSRTFSHLIL*W*SPVTEEDVRLRHCLGVFSPMFAYASRTDQEC

Parental  FEEAFLPTLQTLANAPASSPLAEIDITNVAELLVDLTRPSGLNPQTKTSQDYQALTVHDNLAMKICNEIL
          FEE..LP.LQTLA.APASSPLAEI.I.NV.ELL.DL.R.S.LNPQ.K.S.DYQALTVHD.LA.KIC.EIL
Retrocopy FEEVSLPSLQTLASAPASSPLAEIHIRNVVELLIDLMRTSRLNPQAKNS*DYQALTVHDSLAIKICREIL

Parental  TSPCSPEIRVYTKALSSLELSSHLAKDLLVLLNEILEQVKDRTCLRALEKIKIQL-EKGNKEFGDQAEAA
          TSPCSPE.RV..KALSSLEL.SHLAKDLLVLLN.ILEQVKD...L.ALEKIKIQL..KGNKEFGDQ.EAA
Retrocopy TSPCSPEMRVSIKALSSLELNSHLAKDLLVLLNGILEQVKDGARLKALEKIKIQL>QKGNKEFGDQPEAA

Parental  QDASLTTTTFQNEDEKNKEVYMTPLRGVKATQASKSTQLKTNRGQRKVTVSARTNRRRQTAEADSESDHE
          QDA.LTTT.FQNEDEKNKEV.MT..R.VKAT.ASKS.Q.KTNRGQRKVT.SAR..RR.Q.AEADSESDHE
Retrocopy QDANLTTTIFQNEDEKNKEVHMTLVRDVKATLASKSSQQKTNRGQRKVTASARKKRRHQIAEADSESDHE

Parental  VPEPESEMKMRLPRRAKTAALEKSKLNFAQFLNEDVS
          V.EPESEMKM.LPR.AKTA.LEKSK.N.AQFLNED.S
Retrocopy VLEPESEMKMKLPRQAKTAVLEKSKPNLAQFLNEDLS

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	0.78 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.40 RPM
SRP007412_cerebellum	0.00 RPM	1.23 RPM
SRP007412_heart	0.00 RPM	0.47 RPM
SRP007412_kidney	0.00 RPM	1.06 RPM
SRP007412_liver	0.12 RPM	0.67 RPM
SRP007412_testis	0.04 RPM	54.99 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2370 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2370 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2370 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000018070	1 retrocopy	retro_mmul_2370 ,
Nomascus leucogenys	ENSNLEG00000016632	1 retrocopy	retro_nleu_582,
Pongo abelii	ENSPPYG00000014630	1 retrocopy	retro_pabe_3369,