RetrogeneDB ID: retro_mmul_2621

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:98831119..98831900(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDSPL2
• Ensembl ID: ENSMMUG00000016742
• Aliases: None
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2 [Source:RefSeq peptide;Acc:NP_001253738]

Sequence

>retro_mmul_2621
CAAACAACAACAAAAACCCACAATGGTTTAGAAGAAGCAGAAGAAACAGTTAATCGTGATATCCCACCCCTTATAGGACC
AGTCATTCCAGATAGTGGTTATTCATCAGCCCACGCAGAGGCCACCTATGAAGAAGGCTTGGAAGTATTTGACCCCTATT
ATTTCATCAAACATGTCCTACCACTGACAGAAGAACAACTAAATAGGAAATCTGTTCTTCATTGAAAACAAGAAGCACAC
CGAAATTCTCCCTAGATTTAGACTTGGATGAAACAGTGGTGCACTGTAGTCTAAATGAGGTAGAAGATGCAGCACTTACT
TTTCCAGTCCTTTTCCACGATGTCATTTATCAGGTTTATGTGATATTAATACATTTTTCAGGGAATTCCTGGAATGAATT
TCTCAGATGTATGATATTATTCTTTTTACTGCTTCTAAGAAGGTGTGTGCAGGCACATTACTGAACATAGTAGACCCTGA
AAAGCAAGTGGTCAGGCACCATTTTTTCTGTGAACATTGTGTTTGTGTACAAGGAAATCATATATAGAACTTAAATATTC
TTGGAAGAGATCTTTCAAAAACTGTAATAATTGACAACCCACCACAAACCTTTGCATACAAGCTTTCTAATGGAACCCCT
ATAGAAAGTTGGTTTATGGATAAAAATGACAATGAACTCCTAAAATTGATTTCATTCCTGGAGAAGCTTGTAGAACTGAG
TGAAGATATTCAACTACATATCAGAGACAGATTTCACTTGCATGATTTGCTGACCCAAGAT

Alignment

ORF - retro_mmul_2621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.85 %
• Parental protein coverage: 56.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVRPSINNGLEEAEETVNRDIPPLTAPVTPDSGYSSAHAEATYEEDWEVFDPYYFIKHVPPLTEEQLNRK
          Q......NGLEEAEETVNRDIPPL..PV.PDSGYSSAHAEATYEE..EVFDPYYFIKHV.PLTEEQLNRK
Retrocopy QTTTKTHNGLEEAEETVNRDIPPLIGPVIPDSGYSSAHAEATYEEGLEVFDPYYFIKHVLPLTEEQLNRK

Parental  PAL-PLKTRSTPEFSLVLDLDETLVHCSLNELEDAALTFPVLFQDVIYQVYVRL-RPFFREFLERMSQMY
          ..L..LKTRSTP.FSL.LDLDET.VHCSLNE.EDAALTFPVLF.DVIYQVYV.L...FFREFLE..SQMY
Retrocopy SVL<SLKTRSTPKFSLDLDLDETVVHCSLNEVEDAALTFPVLFHDVIYQVYVIL<NTFFREFLE*ISQMY

Parental  EIILFTASKKVYADKLLNILDPKKQLVRHRLFREHCVCVQGNYIKDLNILGRDLSKTIIIDNSPQAFAYQ
          .IILFTASKKV.A..LLNI.DP.KQ.VRH..F.EHCVCVQGN.I..LNILGRDLSKT.IIDN.PQ.FAY.
Retrocopy DIILFTASKKVCAGTLLNIVDPEKQVVRHHFFCEHCVCVQGNHI*NLNILGRDLSKTVIIDNPPQTFAYK

Parental  LSNGIPIESWFMDKNDNELLKLIPFLEKLVELNEDVRPHIRDRFRLHDLLPPD
          LSNG.PIESWFMDKNDNELLKLI.FLEKLVEL.ED...HIRDRF.LHDLL..D
Retrocopy LSNGTPIESWFMDKNDNELLKLISFLEKLVELSEDIQLHIRDRFHLHDLLTQD

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	18.26 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.31 RPM
SRP007412_cerebellum	0.00 RPM	24.80 RPM
SRP007412_heart	0.00 RPM	6.24 RPM
SRP007412_kidney	0.00 RPM	9.74 RPM
SRP007412_liver	0.00 RPM	3.44 RPM
SRP007412_testis	0.00 RPM	22.92 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2621 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2621 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4881

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002423	1 retrocopy	retro_cjac_4201,
Homo sapiens	ENSG00000137770	1 retrocopy	retro_hsap_4881,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208, retro_mmul_764,
Macaca mulatta	ENSMMUG00000016742	1 retrocopy	retro_mmul_2621 ,