RetrogeneDB ID: retro_mmul_2500

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:63882815..63884218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.895
• Ensembl ID: ENSMMUG00000013973
• Aliases: None
• Description: T-complex protein 1 subunit delta [Source:UniProtKB/TrEMBL;Acc:F6S025]

Sequence

>retro_mmul_2500
GATATGACCATTACATATGATGCTGCCACCATTCTGAAACAAATGTAAGTGTTACATGCAGCAGCCAGAATCCTAGTGGT
GCTGTCTAAGGCTCCAAGATATAGAAGTTGGAGATGGCACCACATCAGTGGTCATTATTGCTGGATCTCTCTTATAGTCC
TATAATAAGCTTCTTCAGAAAGGGATTCATCTAGCCATCATCTCTGAGTCATTCTAGAAGGCTTTGGGAAATGGTATTAA
AGTTGTAACTGACATGTCTTAACCTATGGAAGTAAATGACAAAGAAACATTTTAAAATAGTATAACCAACTTATTGAACT
CAGTGCTTATTTTTCAGTACTCCAGTCTAATTTATCCAATGAATATAGATACAGTGATTAAAGCAAGTGATCTAGCCACA
GCTACCATTGTGTATCTTAGGGATATGAAAGTAGTTAAGTAACTTGGTGGGACAGTTGATTGCAGTGAGTTAGTGAAAGG
GATTATGACCCAAAAGGTGGAAAATTCTGGGATAGCCAGAGTTGAAAAGGCTAAAACTGGGCTTATTCAGTTTTGCTTCT
CTGCTCCCAGAACAGATGGATAATCAAATAGTTTCAGACTTACCCATGTGGAACAAGTGTTGTGAAAAGAAAGAGCCTAA
TACTAAATTTAGTTAAAAAAAAAAAAACTGAAGATAACATCCTGCTCACACAGAAGTCTCTTCTAATTGGTGCTCTTAGT
GATCTTGATTTACGTTTTCTAAACAAAATGAAGATTATGGTGATTAAGGATATTGAAAAATAAGGCATTGAATTTATTTG
TAAGACAACTGGAAACAAGCCAGTTGCTTATATTGACTAATTCACTACTAACATGGTGGGTTCTGCTCCTTTAGCCAAGG
AGGTCAATTTAAATGGTTCTGGCAAATTGCTCAAGACTGCAGGCTATGCACGCCCTGGAAAAGCAGTTATAGTTGTTGTT
CTTCATTCTAATAAACTGATTATTGGAAAGCTAAATGCTCCATTTATGATACCCTATGTTTTATTTCCTGTTTAGTGAAG
AATAGAGTTCTTATTACAAGAGATGGTGCTCCAGAAATCAGAGCTAGCTCTAAAATTACCTGAATATTCATTAACATTGA
GAGGTATGGAATCCTACTGCATTTATGACTTACAGATGATATGGAGGTAACTTCATTTACAGTAGCTAAAAACACTGGCC
TGAATCACATTTCTTCATTAGCAGAACTAGGAAATCAATATGCATAAGAAATAAATACTGTAGGTATTACTGTCCAAAAG
GGTGACATTCTTAACATTTTAGAAGTAATTATTGCCCGACCTCTGTTGGTTTCAATTGGTGCCCTGACTTTAGCAACTGA
AAGTCTCTGAGGCATTCTGAAACTGGATGATATGGTAAACACT

Alignment

ORF - retro_mmul_2500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.47 %
• Parental protein coverage: 94.97 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DVTITNDGATILKQMQVLHPAARMLVELSKA-QDIEAGDGTTSVVIIAGSLLDSCTKLLQKGIHPTIISE
          D.TIT.D.ATILKQM.VLH.AAR.LV.LSKA.QDIE.GDGTTSVVIIAGSLL.S..KLLQKGIH..IISE
Retrocopy DMTITYDAATILKQM*VLHAAARILVVLSKA>QDIEVGDGTTSVVIIAGSLL*SYNKLLQKGIHLAIISE

Parental  SFQKALEKGIEILTDMSRPVELSDRETLLNSATTSLNSKVVSQYSSLLSPMSVNAVMKVIDPATATSVDL
          SF.KAL..GI...TDMS.P.E..D.ET..NS.T..LNS....QYSSL..PM....V.K..D.ATAT.V.L
Retrocopy SF*KALGNGIKVVTDMS*PMEVNDKETF*NSITNLLNSVLIFQYSSLIYPMNIDTVIKASDLATATIVYL

Parental  RDIKIVKKLGGTIDDCELVEGLVLTQKVSNSGITRVEKAKIGLIQFCLSA-PKTDMDNQIVVSDY-AQMD
          RD.K.VK.LGGT.D..ELV.G...TQKV.NSGI.RVEKAK.GLIQFC.SA.P...MDNQIV.SD......
Retrocopy RDMKVVK*LGGTVDCSELVKG-IMTQKVENSGIARVEKAKTGLIQFCFSA>PE-QMDNQIV-SDL<THVE

Parental  RVLREERA-YILNLVKQIKKTGCNVLLIQKSILRDALSDLALHFLNKMKIMVIKDIEREDIEFICKTIGT
          .VL..ERA..ILNLV........N.LL.QKS.L..ALSDL.L.FLNKMKIMVIKDIE...IEFICKT.G.
Retrocopy QVL*KERA<LILNLVXXXXXED-NILLTQKSLLIGALSDLDLRFLNKMKIMVIKDIEK*GIEFICKTTGN

Parental  KPVAHIDQFTADMLGSAELAEEVSLNGSGKLLKITGCASPGKTVTIVVRGSNKLVIE-EAERSIHDALCV
          KPVA.ID.FT..M.GSA.LA.EV.LNGSGKLLK..G.A.PGK.V..VV..SNKL.I...A..SI.D.LC.
Retrocopy KPVAYID*FTTNMVGSAPLAKEVNLNGSGKLLKTAGYARPGKAVIVVVLHSNKLIIG<KAKCSIYDTLCF

Parental  IRCLVKKRALIAGGGAPEI-ELALRLTEYSRTLSGMESYCVRA-FADAMEVIPSTLAENAGLNPISTVTE
          I.CLVK.R.LI...GAPEI.ELAL.L.EYS.TL.GMESYC......D.MEV...T.A.N.GLN.IS...E
Retrocopy ISCLVKNRVLITRDGAPEI>ELALKLPEYSLTLRGMESYCIYD<LTDDMEVTSFTVAKNTGLNHISSLAE

Parental  LRNRHAQGEKTSGINVRKGGISNILEELVVQPLLVSVSALTLATETVRSILKIDDVVNT
          L.N..A....T.GI.V.KG.I.NILE.....PLLVS..ALTLATE....ILK.DD.VNT
Retrocopy LGNQYA*EINTVGITVQKGDILNILEVIIARPLLVSIGALTLATESL*GILKLDDMVNT

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	88.74 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	78.14 RPM
SRP007412_cerebellum	0.13 RPM	82.14 RPM
SRP007412_heart	0.00 RPM	45.64 RPM
SRP007412_kidney	0.00 RPM	57.63 RPM
SRP007412_liver	0.00 RPM	37.80 RPM
SRP007412_testis	0.00 RPM	141.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2500 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2500 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003083	2 retrocopies	retro_cfam_2093, retro_cfam_590,
Callithrix jacchus	ENSCJAG00000008703	1 retrocopy	retro_cjac_724,
Equus caballus	ENSECAG00000016982	1 retrocopy	retro_ecab_148,
Microcebus murinus	ENSMICG00000015263	1 retrocopy	retro_mmur_344,
Macaca mulatta	ENSMMUG00000013973	1 retrocopy	retro_mmul_2500 ,
Monodelphis domestica	ENSMODG00000002882	1 retrocopy	retro_mdom_1402,
Otolemur garnettii	ENSOGAG00000003974	2 retrocopies	retro_ogar_1041, retro_ogar_1931,
Sorex araneus	ENSSARG00000010539	1 retrocopy	retro_sara_7,