RetrogeneDB ID: retro_mmul_1549

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:182289856..182290689(-)
• Located in intron of: ENSMMUG00000000623

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTAP
• Ensembl ID: ENSMMUG00000001137
• Aliases: MTAP, MTAPase
• Description: S-methyl-5'-thioadenosine phosphorylase [Source:UniProtKB/Swiss-Prot;Acc:F6RQL9]

Sequence

>retro_mmul_1549
ATGGCCTCAAGCACCACCACCACCGCCATGAAGATTGTAATAATTGGTGGAACAGGTCTGGATGATCCAGAAATTTTAGA
AGGAAGAACTGAAAAATATGTGGATACTTCATTTGGCAAGCCATCTGATGCCTTAATTTTGGGGAAGATAAAAAAGTGTT
GATTGTGTCCTCCTTGCAAGGCATGGGAGGCAGCACACCATCATGCCTTCCAAGGTCAGCTACCAGGCGAACATCTGGGC
TTTGAAGGAAGAGGGCTGTACTCATGTCATAGGGACCACAGCTTGTGGCTTCTTGAGGGAGGAGATTCAACCTGGCGATA
TTGTCATAATTGATCAGTTCATTGACAGGACCTCTTTGAGACCTCAGTCCTTCTATGATGGAAGTCATTCTTGTGCCAGA
GGACTGTGCCATATTCCAATAGCCAAGCCATTTTGCCCCCAAATGAGAGAGGTTCTTATAGAGATGGCTAAGAAGCTAGG
ACTCTGGTGCCATTCAAAGGGGACAATGGTCACAACTGAGGGACTTTGTTTTAGCTCTTGGGCAGAAAGCTTCGTGTTCT
GCACCTGGGGGTGGATGCTATCAACATGCCTACAGTTCCAGAGGCAGCCCTTGCTAGGGAGGCTGGAATTTGGTATGCGA
ATATCGCCATGGTGACAGATTATGACTGGTGGAAGGAGTACAAGGAAGTAGTTCTGGTGGACCAGGACTTAAAGACCCTG
AAAGAAAATGCTAGTAAAGCCAAAAGTTTACTGCTCACTACCATACCTCAGTAGGGTCCATGGAATGGTCAAAAACCCTC
TAGAGCCTGAAGAATATAGCCCAGTTTTCTGTT

Alignment

ORF - retro_mmul_1549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.56 %
• Parental protein coverage: 98.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASGTTTTAVKIGIIGGTGLDDPEILEGRTEKYVDTPFGKPSDALILGKIK-NVDCVLLARHGRQHTIMP
          MAS.TTTTA.KI.IIGGTGLDDPEILEGRTEKYVDT.FGKPSDALILGKIK..VDCVLLARHGRQHTIMP
Retrocopy MASSTTTTAMKIVIIGGTGLDDPEILEGRTEKYVDTSFGKPSDALILGKIK>SVDCVLLARHGRQHTIMP

Parental  SKVNYQANIWALKEEGCTHVIVTTACGSLREEIQPGDIVIIDQFIDRTTMRPQSFYDGSHSCARGVCHIP
          SKV.YQANIWALKEEGCTHVI.TTACG.LREEIQPGDIVIIDQFIDRT..RPQSFYDGSHSCARG.CHIP
Retrocopy SKVSYQANIWALKEEGCTHVIGTTACGFLREEIQPGDIVIIDQFIDRTSLRPQSFYDGSHSCARGLCHIP

Parental  MAEPFCPKTREVLIETAKKLGLRCHSKGTMVTIEGPRFSSRAESFMFRTW-GADVINMTTVPEVVLAKEA
          .A.PFCP..REVLIE.AKKLGL.CHSKGTMVT.EG..FSS.AESF.F.TW.G.D.INM.TVPE..LA.EA
Retrocopy IAKPFCPQMREVLIEMAKKLGLWCHSKGTMVTTEGLCFSSWAESFVFCTW<GVDAINMPTVPEAALAREA

Parental  GICYASIAMATDYDCWKEHEEAVSVDRVLKTLKENANKAKSLLLTTIPQ-IGSTEWSETLHNLKNMAQFS
          GI.YA.IAM.TDYD.WKE..E.V.VD..LKTLKENA.KAKSLLLTTIPQ..GS.EWS.TL..LKN.AQFS
Retrocopy GIWYANIAMVTDYDWWKEYKEVVLVDQDLKTLKENASKAKSLLLTTIPQ<VGSMEWSKTL*SLKNIAQFS

Parental  V
          V
Retrocopy V

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	4.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.09 RPM
SRP007412_cerebellum	0.00 RPM	2.84 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.12 RPM	5.28 RPM
SRP007412_liver	0.00 RPM	6.37 RPM
SRP007412_testis	4.15 RPM	23.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1549 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1549 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002224	1 retrocopy	retro_chof_772,
Callithrix jacchus	ENSCJAG00000008021	2 retrocopies	retro_cjac_187, retro_cjac_950,
Cavia porcellus	ENSCPOG00000000825	1 retrocopy	retro_cpor_375,
Dasypus novemcinctus	ENSDNOG00000008670	1 retrocopy	retro_dnov_1572,
Echinops telfairi	ENSETEG00000013214	1 retrocopy	retro_etel_588,
Macropus eugenii	ENSMEUG00000015381	2 retrocopies	retro_meug_807, retro_meug_917,
Microcebus murinus	ENSMICG00000015072	1 retrocopy	retro_mmur_927,
Macaca mulatta	ENSMMUG00000001137	1 retrocopy	retro_mmul_1549 ,
Ornithorhynchus anatinus	ENSOANG00000013963	1 retrocopy	retro_oana_38,
Oryctolagus cuniculus	ENSOCUG00000012289	2 retrocopies	retro_ocun_1355, retro_ocun_341,
Otolemur garnettii	ENSOGAG00000007889	1 retrocopy	retro_ogar_3285,
Ochotona princeps	ENSOPRG00000001259	1 retrocopy	retro_opri_792,