RetrogeneDB ID: retro_mmul_1926

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:175497865..175499111(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHN2
• Ensembl ID: ENSMMUG00000008329
• Aliases: None
• Description: beta-chimaerin [Source:RefSeq peptide;Acc:NP_001248506]

Sequence

>retro_mmul_1926
GAAAACAGCCCGAAGTATCATGGAAGAGAGTTTCACGGCATGATCTCCGGAGAAGCAGCTGACCAGCTCTTGAGTGTGGC
TGAGGGAGATACATCATGGGGAGAGGCAGCAACAGCCAGGGTTCTACACTTTGGCTTTCAGATTGGGAAGTCAAGCAAGA
AACTTGAGGCTCTAGTGCAATGGAAATCACTTTGCAGGGGAAAAACACTGTGTGTCCACCCACAGTCTGGTAACTGATGG
CTTGATTACTCTCTATATTGAAACAAAGCAGCAGAATACATTGCCAAGGTGATGATAAACCCAGTTTATGAACACATAGG
ATGCACAACCTTAAACAGAGTGTCTGCTGGCAAAAAATATATGCCAGTCCTGAAAGAGACATGTGGTGAGATTCTACAGG
CCAGGATGAGGTGTTGGAGAAAAGACTGACATCACTTGTTAGAAGAGCAACTCTGAAAGAAAACGAGCAAATTCCAAAAT
ATGAGAAGGTTCACAATTTCAAGGTCCATGGATCGAGAGGCCCATGCTAGCGTAAATACTGTGACATCTTCATGTATGGT
CTCATTGCTCAGGGAGTGAACCATGTGGATTGGTTTCAGTGTTCACAAGCAGTGACCCCACATGGTCCCAAATGACTGGA
AAGCAGGCTTGAGGCATGCCAGCGTGTCCAGCTGTGACCTTACAGTGCTTGTCAAAAGCACACACCTTGGCTAAGCGGCC
AAGGGTGGTGGACATGTGCAACAGGGAGATTGAGTTTGAAAGTCCCAATTCTGAAGGGCTATACCATGTATCAGGATTTA
GTGACTTAACTGATGTCAAGACGGCTTTTGACAGAGGTGGTGAGAAAGCAGCTATTTCTGTGAACACATACAAAGACATC
AACATTATCACTGGAACTCAGAAACCGCACTTCAGGGATTTGCCAATTTCACTAATTACGCATGATATCTACCCTAAATT
TATAGAATCTGCCAAAACTATGGATCCTAGTGAGTAACTGGAAACCCTTCATGAAGCATTGAAACTACTGGCACCTGCTC
GCTGTGAAACCCTCTGATCCCTGATGGCGCATCTAAACAGAGTGACACTCCATGAAAAGGAAAATCTTGTAAATGCGGAG
AGCCATGGAATTGTCTTTGGCCCATCCCTTCTGAGACCTCCAGAATGAAATGCCATGGCTGCATTGAACAATATACAATA
TCAGAGACTGGTGGTGGAGCTGCTTATCAAAAACGGAGACATTTTA

Alignment

ORF - retro_mmul_1926 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.36 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ENRPKYYGREFHGIISREQADELLGGVEG-AYILR-ESQRQPGCYTLALRFGNQTLNYRLFHDGKHFVGE
          EN.PKY.GREFHG.IS.E.AD.LL...EG..YI...E.Q.QPG.YTLA.R.G.Q..N.RL...G.HF.GE
Retrocopy ENSPKYHGREFHGMISGEAADQLLSVAEG<RYIMG<ERQQQPGFYTLAFRLGSQARNLRL*CNGNHFAGE

Parental  KRFESIHDLVTDGLITLYIETK-AAEYISKMTTNPIYEHIGYATLLREKVSR-KLSKSKNEPRKTNVTHE
          K...S.H.LVTDGLITLYIETK.AAEYI.K...NP.YEHIG..TL.R......K...S.........T..
Retrocopy KHCVSTHSLVTDGLITLYIETK<AAEYIAKVMINPVYEHIGCTTLNRVSAGK<KIYASPERDMW*DSTGQ

Parental  EHTAVDKISSLVRRAALTHNDNHFNYEKTHNFKVHTFRGPHWCEYCANFMWGLIAQGVRCSDCGLNVHKQ
          .........SLVRRA.L..N.....YEK.HNFKVH..RGP....YC..FM.GLIAQGV...D........
Retrocopy DEVLEKRLTSLVRRATLKENEQIPKYEKVHNFKVHGSRGPC*RKYCDIFMYGLIAQGVNHVD-WFQCSQA

Parental  CSKHVPNDCQPDLKRIKKVY-CCDLTTLVKAHN-TQRPMVVDICIREIEARGLKSEGLYRVSGFTEHIED
          ...H.P......L.....V.....L..L.KAH....RP.VVD.C.REIE.....SEGLY.VSGF.....D
Retrocopy VTPHGPK*LESRLEACQRVQ<AVTLQCLSKAHTLAKRPRVVDMCNREIEFESPNSEGLYHVSGFSD-LTD

Parental  VKMAFDRDGEKADISANVYPDINIITGALKLYFRDLPIPVITYDTYSKFIDAAKISNADERLEAVHEVLM
          VK.AFDR.GEKA.IS.N.Y.DINIITG..K..FRDLPI..IT.D.Y.KFI..AK.....E.LE..HE.L.
Retrocopy VKTAFDRGGEKAAISVNTYKDINIITGTQKPHFRDLPISLITHDIYPKFIESAKTMDPSE*LETLHEALK

Parental  LLPPAHYETLRYLMIHLKKVTMNEKDNFMNAENLGIVFGPTLMRPPEDSTLTTLHDMRYQKLIVQILIEN
          LL.PA..ETL..LM.HL..VT..EK.N..NAE..GIVFGP.L.RPPE......L....YQ.L.V..LI.N
Retrocopy LLAPARCETL*SLMAHLNRVTLHEKENLVNAESHGIVFGPSLLRPPE*NAMAALNNIQYQRLVVELLIKN

Parental  EDVL
          .D.L
Retrocopy GDIL

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	55.35 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	54.34 RPM
SRP007412_cerebellum	0.00 RPM	296.72 RPM
SRP007412_heart	0.00 RPM	2.47 RPM
SRP007412_kidney	0.00 RPM	19.01 RPM
SRP007412_liver	0.00 RPM	46.08 RPM
SRP007412_testis	0.00 RPM	38.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1926 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1926 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1926 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003023	1 retrocopy	retro_cfam_2185,
Macaca mulatta	ENSMMUG00000008329	1 retrocopy	retro_mmul_1926 ,
Oryctolagus cuniculus	ENSOCUG00000009401	1 retrocopy	retro_ocun_440,
Sus scrofa	ENSSSCG00000016687	1 retrocopy	retro_sscr_939,