RetrogeneDB ID: retro_mmul_1294

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:59414411..59416033(+)
• Located in intron of: ENSMMUG00000030682

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2698
• Ensembl ID: ENSMMUG00000020112
• Aliases: None
• Description: T-complex protein 1 subunit epsilon [Source:RefSeq peptide;Acc:NP_001245118]

Sequence

>retro_mmul_1294
ATGGCATCCATGGAGACCCTCGCCTTCGATTGATATGGGCCCCCTTTCCTCATCAGCAAGGATCAGGACCACAAGTCCCG
CCTTATGGGACTTGAGGCCCTCAAGTCTCATATAGTGGCAGCAAAGGCTGTAGCAAATACAATGAGAACATCACTTGGAC
CAAATGGGCTTGATAAGATGATGGTGGATAAGGATGGCGATGTGACTGTAAGTAATGATGGGGTCACCATCTTAAGCATG
ATAGATGTCGACCATCAGATTGCCAAGCTGATGGTGGAAATGTCCAAGTCTCAGGATGATGAAATTGGAGATGGAACCAC
AGGAGTGGTTGTCCTGGCTGGTGCCTTGTTAGAATAAGCCCAGGAGTTGCTAGACCAAGGTATTCACCCAATCAGAATAG
CTGGTGGCTATGAGCAGGCTGCCTGTGTTGCTATTGAACACCTGGACAAGATCAGCGATAGCATCCTTGTTGATGTAAAG
GACACCAAATCCCTGATTCAGACTGCAGAAACCATGCTGAGCTCCAAAGTGATCAACAGTTGTCACTGACAAATGGCTGA
GATTGCTGTGAATGCCGTCCTTACTGTAACAGATATGGAGCAGAGAGGTGTTGACTTTGAGCTTATCAAAGTAGAAAGCA
AAGTGGGTGGCAGGCTGGAGGACACTAAATGGATTAAGGACATGATTGTGGACAAGGATTTCAGTCACCCACAGATGCCA
AAAAAGTGGAAGATGCTAAGATTGTAATTCTCACATGTCCATTTGAATACCCAAACCAAAAACAAAGCATAAGCTGGATG
TGACCTCTGTAGAAGATCATAAAGCCCTTCAGAAATATGAAAAGGAGACATTTTAAGAGATGATTCAACAAATTAAAGAG
ACTGGTGCTAAAATAGAAATTTGTCAGTGGGACTTTGATGATGAAGCAAATCACTTACTTCTTCAGAACAACTTGCCTGT
GGTTCGCTGGGTAGGAGGACCTGAAATTGAACTGATTGCCATCACAACAGGAGGGCAGATCACCCCCAAGTTCTCAGAGC
TCTCGGCCAGGAAGCTGGGCTTTGCTGGTCTTGTACAGGAGATCTCATTTGGGACAACTAAGGATAAAATGCTGGTCATT
GAGCAGTGTAAGAACTCCAGAGCTGTAATCATTTTTATGAGAAGAGGAAATAAGATGAGTATTGAGGAGGTGAAACAACC
CCTTCATGATGCTTTGTGTGTCATCTGGAAGCTCATCCATGATAATCATATGGTGTGTGGAGGAGGGGCTGCTGAGATAT
CCTGTGCCCTGCCAGTTAGCCAAGAGGTTGATAAGTGCCCCACCTTAGAACTCTATGCCTTGAGAGCATTTGCCGACGCT
TTGGAGGTCATTCCCAAGGCCCTTTCTGAAAACAGTGGCATGAATCCCATCCAGACTATGACCGAAGCCCAAGCCAGACA
AGTAAATGAGAGGAACCTTGCTCTTGGCATCGACTGTTTGCACAAGGGAACAAATGATATGAAGCAATAGCATGTCATAG
AAACCTTCATTGGCAAAAAAGCAACAGATATCTCTTGCAACACAAATGGTTAGAATGATTTTGAAGATTGACAACATTCG
TAAGCCTGGAGAATCTGAAGAA

Alignment

ORF - retro_mmul_1294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASMGTLAFDEYGRPFLIIKDQDRKSRLMGLEALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVTV
          MASM.TLAFD.YG.PFLI.KDQD.KSRLMGLEALKSHI.AAKAVANTMRTSLGPNGLDKMMVDKDGDVTV
Retrocopy MASMETLAFD*YGPPFLISKDQDHKSRLMGLEALKSHIVAAKAVANTMRTSLGPNGLDKMMVDKDGDVTV

Parental  TNDGATILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQA
          .NDG.TILSM.DVDHQIAKLMVE.SKSQDDEIGDGTTGVVVLAGALLE.A..LLD.GIHPIRIA.GYEQA
Retrocopy SNDGVTILSMIDVDHQIAKLMVEMSKSQDDEIGDGTTGVVVLAGALLE*AQELLDQGIHPIRIAGGYEQA

Parental  ARVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLGSKVVNSCHRQMAEIAVNAVLTVADMERRDVDFELIK
          A.VAIEHLDKISDS.LVD.KDT..LIQTA.T.L.SKV.NSCH.QMAEIAVNAVLTV.DME.R.VDFELIK
Retrocopy ACVAIEHLDKISDSILVDVKDTKSLIQTAETMLSSKVINSCH*QMAEIAVNAVLTVTDMEQRGVDFELIK

Parental  VEGKVGGRLEDTKLIKGVIVDKDFSHPQMPKK-VEDAKIAILTCPFEPP-KPKTKHKLDVTSVEDYKALQ
          VE.KVGGRLEDTK.IK..IVDKDFSHPQMPKK.VEDAKI.ILTCPFE.P.KPKTKHKLDVTSVED.KALQ
Retrocopy VESKVGGRLEDTKWIKDMIVDKDFSHPQMPKK<VEDAKIVILTCPFEYP<KPKTKHKLDVTSVEDHKALQ

Parental  KYEKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVPRFSEL
          KYEKE.F.EMIQQIKETGA...ICQW.FDDEANHLLLQNNLP.VRWVGGPEIELIAI.TGG.I.P.FSEL
Retrocopy KYEKETF*EMIQQIKETGAKIEICQWDFDDEANHLLLQNNLPVVRWVGGPEIELIAITTGGQITPKFSEL

Parental  TAEKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIRDNRV
          .A.KLGFAGLVQEISFGTTKDKMLVIEQCKNSRAV.IF.R.GNKM.IEE.K..LHDALCVI..LI.DN..
Retrocopy SARKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVIIFMRRGNKMSIEEVKQPLHDALCVIWKLIHDNHM

Parental  VYGGGAAEISCALAVSQEADKCPTLEQYAMRAFADALEVIPMALSENSGMNPIQTMTEVRARQVKEMNPA
          V.GGGAAEISCAL.VSQE.DKCPTLE.YA.RAFADALEVIP.ALSENSGMNPIQTMTE..ARQV.E.N.A
Retrocopy VCGGGAAEISCALPVSQEVDKCPTLELYALRAFADALEVIPKALSENSGMNPIQTMTEAQARQVNERNLA

Parental  LGIDCLHKGTNDMKQQHVIETLIG-KKQQISLATQMVRMILKIDDIRKPGESEE
          LGIDCLHKGTNDMKQ.HVIET.IG.KKQQISLATQMVRMILKID.IRKPGESEE
Retrocopy LGIDCLHKGTNDMKQ*HVIETFIG>KKQQISLATQMVRMILKIDNIRKPGESEE

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	66.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	69.89 RPM
SRP007412_cerebellum	0.00 RPM	63.09 RPM
SRP007412_heart	0.00 RPM	73.02 RPM
SRP007412_kidney	0.00 RPM	88.14 RPM
SRP007412_liver	0.08 RPM	63.69 RPM
SRP007412_testis	0.30 RPM	362.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1294 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1294 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1219
Pan troglodytes	retro_ptro_834
Pongo abelii	retro_pabe_1012

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008977	1 retrocopy	retro_cjac_516,
Homo sapiens	ENSG00000150753	2 retrocopies	retro_hsap_1219, retro_hsap_3230,
Gorilla gorilla	ENSGGOG00000024064	1 retrocopy	retro_ggor_2197,
Macaca mulatta	ENSMMUG00000020112	2 retrocopies	retro_mmul_1294 , retro_mmul_2033,
Monodelphis domestica	ENSMODG00000002356	1 retrocopy	retro_mdom_861,
Pan troglodytes	ENSPTRG00000016725	2 retrocopies	retro_ptro_2182, retro_ptro_834,
Tupaia belangeri	ENSTBEG00000001201	2 retrocopies	retro_tbel_1618, retro_tbel_4389,