RetrogeneDB ID: retro_mmul_1193

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:72100425..72101694(-)
• Located in intron of: ENSMMUG00000014558

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGHE
• Ensembl ID: ENSMMUG00000030305
• Aliases: None
• Description: None

Sequence

>retro_mmul_1193
GCCTCCAGACAGGGCCCATCTGTCTTCCCCTTGTTCCCCTCCTGCAAAGACATTGCCTCCGATGCCACCTCCATGACCCT
GGGCTGCCTGGCCACAGGCTAGTTCCTGAAGCCGGTGACTGTGACCTGGGACACAGGCTACCTCAACAGGAGTGCTGTGA
CCTTCCCAGCCACCACCCTCACACCCTCTGGCCACTACGCCACCACCAGCCATCTGACCACCTCAGGTGCATGGACCAAG
CAAATGTTCACCTGTAGCATGGTACACACTCTGTGGTCTGCAGACCAGGTCAGTACCTTCAGCGTCTACTCTAGGGACTT
CGCCCTGCCCACCATGAAGATCTTACAGTCCTGTGATGGCAGTGGACACTTCCCCCCGACCATCCAGTTCCTGTGCCTCA
CTTCCGGGTACACCCCAGGTGCCATCACCTGGCTGGAGGATGGGCAGGTCGTGGATGTGAACTGCTCTATTGCCTCTCCC
ATGCTGGAGGGCGAGCTGGCCTCCACACAAAGCAAGCTCACCCTCACCCAGAAGCTTTGGCTGCCCGACCACACCTACAC
CTGCCAGGTCACCTATCAAGGTAATGCCTTTGAGGACAGTGCCAAGAAGCATGCAGATTCCAACCCGCAAGGGGTGAGTG
CCTACCTGAGCTAGCCCAGCCCCTTCTACCTGTTCATCCGCAAGTTGCCCACAATCACCTGTCTGGTGGTGGACCTGGCA
CCTAGCAAGGGGACCGTGAAGCTGACCTGGTCCCGGGCCAGTGGGAAGTCCGTGGCCCAGGTCCTCCTAAGGCAAGAGAA
GCAGTGCAGTGGCACGTTCATCATCACGTCCACTCTGCTGGTGGGCACCAGAGACTGGATCGAGGGGGAGACCTACCAGT
GCAGGGTGACCCACCTCCACCTGCCCAGGGCCCTTGTGCAGTCCATGACCAAGATCAGCGACCGCTGTGCTCCCCCAGAG
GTCTACGGGTTTGCAATGCTAGAAGAGCCGAGGAACCCAGACAAGCGCACCCTCACCTGCCTGATCCAGAACTTCTAGCC
CAAGGACATCTTGGTGCAGTTGCTGCACAACAAGGTGCAGCTCCCAGACGCCTGGCACAGCATGACGCAGCCCTGCAAAA
CCAAGGGCTCTGGCTTCTTAGTCTTCAGCTGCCTGGAGGTGACCAGGGCCGAATGGGAACAGAAAAATGAGTTCATCTGC
CCTGTGGTCCATGAGATGGTGACTGGCTCACAGACCGTCAAGAAGCTGGTGTCTGTAAATCCCATTAAA

Alignment

ORF - retro_mmul_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASIQSPFVFPLIPCCKHIASNATSVTLGCLATGYFPEPVMVTWDAGSLNRSTMTLPATTFTPSGHYATIS
          AS.Q.P.VFPL.P.CK.IAS.ATS.TLGCLATG.F..PV.VTWD.G.LNRS..T.PATT.TPSGHYAT.S
Retrocopy ASRQGPSVFPLFPSCKDIASDATSMTLGCLATG*FLKPVTVTWDTGYLNRSAVTFPATTLTPSGHYATTS

Parental  LLTVSGAWAKETFTCHVVHTPSSADKEVNKTFGVCSRNFTPPTVKILQSSCDDDGHFPPTIQLLCLISGY
          .LT.SGAW.K..FTC..VHT..SAD.....TF.V.SR.F..PT.KILQS.CD..GHFPPTIQ.LCL.SGY
Retrocopy HLTTSGAWTKQMFTCSMVHTLWSADQV--STFSVYSRDFALPTMKILQS-CDGSGHFPPTIQFLCLTSGY

Parental  TPGAINVTWLENGQVMKVNSPTPPATQEGELASTQSEFTLAQKQWLTDRNYTCQVTYQGTTYNDSTKKCA
          TPGAI..TWLE.GQV..VN........EGELASTQS..TL.QK.WL.D..YTCQVTYQG....DS.KK.A
Retrocopy TPGAI--TWLEDGQVVDVNCSIASPMLEGELASTQSKLTLTQKLWLPDHTYTCQVTYQGNAFEDSAKKHA

Parental  DSNPRGVSAYLSRPSPFDLFISKSPTITCLVVDLAPSKETVNLTWSRASGKPVPHIPTTEKKQRNGTLTV
          DSNP.GVSAYLS.PSPF.LFI.K.PTITCLVVDLAPSK.TV.LTWSRASGK.V........KQ..GT...
Retrocopy DSNPQGVSAYLS*PSPFYLFIRKLPTITCLVVDLAPSKGTVKLTWSRASGKSVAQVLLRQEKQCSGTFII

Parental  TSILPVVTQDWIEGETYQCRVTHPHLPRALVRSMTKTSGPRAAPEVYVFATPEKLESRDKRTLACLIQNF
          TS.L.V.T.DWIEGETYQCRVTH.HLPRALV.SMTK.S...A.PEVY.FA..E.....DKRTL.CLIQNF
Retrocopy TSTLLVGTRDWIEGETYQCRVTHLHLPRALVQSMTKISDRCAPPEVYGFAMLEEPRNPDKRTLTCLIQNF

Parental  MPEDISVQWLHSDVQLPDARHSVTQPRKTKGSGFFVFSRLEVTKAEWEQKDEFICRAVHEAASPSWIVQQ
          .P.DI.VQ.LH..VQLPDA.HS.TQP.KTKGSGF.VFS.LEVT.AEWEQK.EFIC..VHE....S..V..
Retrocopy *PKDILVQLLHNKVQLPDAWHSMTQPCKTKGSGFLVFSCLEVTRAEWEQKNEFICPVVHEMVTGSQTVKK

Parental  AVSVNPGK
          .VSVNP.K
Retrocopy LVSVNPIK

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	0.11 RPM	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	0.00 RPM
SRP007412_cerebellum	0.19 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.12 RPM
SRP007412_liver	0.59 RPM	0.04 RPM
SRP007412_testis	0.41 RPM	0.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1193 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1193 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2771

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000028496	1 retrocopy	retro_ggor_2771,
Macaca mulatta	ENSMMUG00000030305	1 retrocopy	retro_mmul_1193 ,