RetrogeneDB ID: retro_mmul_1696

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:83483443..83484867(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1934
• Ensembl ID: ENSMMUG00000012846
• Aliases: None
• Description: T-complex protein 1 subunit alpha [Source:RefSeq peptide;Acc:NP_001244657]

Sequence

>retro_mmul_1696
ATGGAGGGACCTTTGTCCGTGTTCGGGGACCCGCAGCACTGGGGAGGCAATCCGCTCCCGGAACGTTATGACTGCAGCTT
CGATTGCCAATATTGTAAAAAGTTCTCTTGGTCCAGTTGGCTTGGATAAAATGTTGGTGGATGATACTGGTGATGTAACC
ATTGCTAAGGATGGTGCACCCATCCTGAAGTTACTGGAGGTAGAACATCCTGCAGCTAAAGTCTTTGTGAGCTGGCTGAT
CTGCAAGACAAAGAAGTTGGAGATGGAACTACCTCAGTGGTTATTATTGCAGCAGAACTCCTAAAAAATGCAGACGAATT
AGTCAAACAGAAAATCCATCCCACATCAGTTATTAGTGGCTATCGACTTGCTTGCAAGGAAGCAGTGCGTTATATCAATG
AAAACGTAATTGTTAACACAGATGAACTGGGAAGAGATTGCCTGATTAATGCTGCTAAGACATCCATGTCTTCCAAAATC
ATTGGAATAAATGGTGATTTCTTTGCTAACATGGTAGGAGATGTTGTACTTGCTATTAAATACACAGATATAAGAGGCCA
GCCACACTATCCAGTCAATTCTGTTAGTATTTCGGAAGCCCATGGGAGAAGTCAAACAAACAGTATGCTCATCAGTGACT
ATGCACTAAACTGTGTGGTGGGATCCCAGGGCATGCCCAAGAGAACTGTAAGTGCAAAAATTGCTTGCCTTGACTTTAGC
CTGCAAAAAACAAAAATGAAGCTTGATGTACAGGTGGTCATTACAGACCCTGAAAAACTGGACCAGATTAGACAGAGAGG
ATCAGATATCACCAACAAGAGAATTCAGAAGATCCTAGCAACTGGTACCGACATTTTCTAACCACTGGTGGAATTAATGA
TACGTGTCTGAAGTATTTTGTGAAGGCTGGTGCTATGGCAGTTAGAAGAGTTTTAAAAAGGGGCCTTAAACACATTGTGA
AAGCTTCTGGAGCAACTATTCTGTCAAGTCTGGCCAATTTGGAAGGTGAAGAAACTTTTGAAGCTGCCTTGGGACTGGCA
AAAGTGGTACAGGAGAGAATTTGTGATGATGAGCTGATCTTAATCAAAAACACTAAGGCTAATACGTCTGCAACGATTAT
CTTATGTAGGGCAAATGATTTCATGTGTGATGAGATTGAGCATTCTTAACATGATGCTCTTTGTGTAGTGAAGATAGTTT
TGGAGTCAAAATCCGTGGTTCCAGGTGGGGATGCTGTAGAAGTAGCCCTTTCCATATACCTTGAAAATTATGCAACCAGC
ATGGGGTCTTGGGAACAGATTGCTACTGCAGAGTTTGCAAGATCACTTCTTGTTATTCCTAATACACTGGCAGTTAATGC
TGCCCAGGACTCTACAGATCTGGATGCAAAATTAAGAGCTTGTCATAATGAGGCTCAGGTTAAC

Alignment

ORF - retro_mmul_1696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 85.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEGPLSVFGD-RSTGEAIRSQNVMAAASIANIVKSSLGPVGLDKMLVDDIGDVTITNDGATILKLLEVEH
          MEGPLSVFGD.RSTGEAIRS.NVM.AASIANIVKSSLGPVGLDKMLVDD.GDVTI..DGA.ILKLLEVEH
Retrocopy MEGPLSVFGD>RSTGEAIRSRNVMTAASIANIVKSSLGPVGLDKMLVDDTGDVTIAKDGAPILKLLEVEH

Parental  PAAKV-LCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENLIV
          PAAKV.LCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINEN.IV
Retrocopy PAAKV<LCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYINENVIV

Parental  NTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAIKYTDTRGQPRYPVNSVNILKAHGRSQMES
          NTDELGRDCLINAAKTSMSSKIIGINGDFFANMV.D.VLAIKYTD.RGQP.YPVNSV.I..AHGRSQ..S
Retrocopy NTDELGRDCLINAAKTSMSSKIIGINGDFFANMVGDVVLAIKYTDIRGQPHYPVNSVSISEAHGRSQTNS

Parental  MLISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVVITDPEKLDQIRQRESDITKERIQKI
          MLIS.YALNCVVGSQGMPKR.V.AKIACLDFSLQKTKMKL.VQVVITDPEKLDQIRQR.SDIT..RIQKI
Retrocopy MLISDYALNCVVGSQGMPKRTVSAKIACLDFSLQKTKMKLDVQVVITDPEKLDQIRQRGSDITNKRIQKI

Parental  LATGANV-ILTTGGIDDMCLKYFVEAGAMAVRRVLKRDLKRIAKASGATILSTLANLEGEETFEAAMLGQ
          LATG.....LTTGGI.D.CLKYFV.AGAMAVRRVLKR.LK.I.KASGATILS.LANLEGEETFEAA.LG.
Retrocopy LATGTDI<FLTTGGINDTCLKYFVKAGAMAVRRVLKRGLKHIVKASGATILSSLANLEGEETFEAA-LGL

Parental  AEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLESKSVVPGGGAVEA
          A..VVQERICDDELILIKNTKA.TSA.IIL..ANDFMCDE.E.S.HDALCVVK.VLESKSVVPGG.AVE.
Retrocopy A-KVVQERICDDELILIKNTKANTSATIILCRANDFMCDEIEHS*HDALCVVKIVLESKSVVPGGDAVEV

Parental  ALSIYLENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSTDLVAKLRAFHNEAQVN
          ALSIYLENYATSMGS.EQ.A.AEFARSLLVIPNTLAVNAAQDSTDL.AKLRA.HNEAQVN
Retrocopy ALSIYLENYATSMGSWEQIATAEFARSLLVIPNTLAVNAAQDSTDLDAKLRACHNEAQVN

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	84.26 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	77.03 RPM
SRP007412_cerebellum	0.00 RPM	73.81 RPM
SRP007412_heart	0.06 RPM	50.52 RPM
SRP007412_kidney	0.00 RPM	54.22 RPM
SRP007412_liver	0.08 RPM	29.45 RPM
SRP007412_testis	0.11 RPM	177.54 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1696 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1696 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3722
Pan troglodytes	retro_ptro_2617
Gorilla gorilla	retro_ggor_2514

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696 ,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Rattus norvegicus	ENSRNOG00000014160	1 retrocopy	retro_rnor_2091,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,