RetrogeneDB ID: retro_mmul_1194

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:72102807..72103953(-)
• Located in intron of: ENSMMUG00000014558

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCF3
• Ensembl ID: ENSMMUG00000009017
• Aliases: None
• Description: None

Sequence

>retro_mmul_1194
GCCTCCTTTGGGAGAGACGCAGGCGTGGGCGGCCTGACTCAGGCTGGCTTCCTGCCGGGCGAGCTGGCCCTCAGCAGCCC
CGGACCCCTGTTCCCTTTGGGCATGAAGGCGACCTCCCAGTACTACCCCTCCTACGCCGGCAGCTCCGGCGGAGAGAGGC
GGACGGCGGCCTGGACACGCAGTCCACAAAGGTCCAGAAGGTCCTGCCTGTCTTCCATCCTCGGCGTACCTGCCCAGCTC
AGGTGAGGACTACGGTAGGGATGCCGCCGCCTACCTGTCCGCCAAGACCCCCAGCAGGGCCTATCCCGCCCCCTTCTACA
TGGCAGATGGCAGGCAGCATACACCCCTCAGCCCCTCAGCCGAGGTCTGGTGTTGCCCGGGTCAGGCGGGCTTTGGCCCC
ATGCTGGGTGGGGGCTCATACCCCCCGCCTCTCCCGCCCAGCAGCTGCCCTGTGGGCAGTGGCAGAGGCAGCAGCACATT
TGGTGGCCTGCACCAGCACGAGCGCATGGGCTACCAGCTGCACAGAGCAGAGGTGAACGGTGGTCTCCCAGCTGCATCCA
CCTTCTCCTTGGCCCCCTGGAGCTGGAGCGTCTCCAGCCACAGGCCACCTGTCAGCGGGGCCAACATATTCCTGGGCTCG
CGAGGGACCACAGCTGGCAGCTCCTGGGACGCCCTCAGGCAGGCATGTCCTCAATCTACTCCCCGGATCACTCAAGCAAT
AGCTTCTCGTCCAGCTCCTCCACTGCTGTGGGCTACCCCCAGGGTCTGGGAGGGATGTCGCACTGGCCCGGAACAGGAGT
CCCCGGTGCCTTATCACCCAGCTACGACGGGGATTTCCATGGCGTGCAGAGTAAGACAGAAGACCACCTGAACAAGGCCA
TCCACGTGCTCTGCAGCCACACCGTGGGCACGGCCGGCAATGGGCCCACGCTGCTGCCCGGCCACAGGGCGCTGGCTTAG
GCTTCGCCGGCCCTATGCTGCTAGTGGGGGCAGCACGCAGGCCTGGTCAGAGGCTGACACCCTGAGGACGGCCCTGTGGG
CAGCGCCAGCCTCATGCACATCCACGTGGCCCTCTCCAGCTAGCCAGGCGCCCTCTCCGACCTCTCTTGGCCTCCCGACT
CCTACAGTGGGCTAGGGCAAGCAGGC

Alignment

ORF - retro_mmul_1194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 58.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ASFGRDAGVGGLTQAGFLSGELALSSPGPLSPSGMKGTSQYYPSYSGSS-RRRAADGSLDTQPKKVRKV-
          ASFGRDAGVGGLTQAGFL.GELALSSPGPL.P.GMK.TSQYYPSY.GSS.RRR.ADG.LDTQ..KV.KV.
Retrocopy ASFGRDAGVGGLTQAGFLPGELALSSPGPLFPLGMKATSQYYPSYAGSS<RRREADGGLDTQSTKVQKV<

Parental  PPGLPSSVYPPSSGEDYGRDAAAYPSAKTPSSAYPAPFYMADGSLH----PSAELWSPPGQAGFGPMLGG
          P..LPSS.Y.PSSGEDYGRDAAAY.SAKTPS.AYPAPFYMADG..H....PSAE.W..PGQAGFGPMLGG
Retrocopy PACLPSSAYLPSSGEDYGRDAAAYLSAKTPSRAYPAPFYMADGRQHTPLSPSAEVWCCPGQAGFGPMLGG

Parental  GSSPLPLPPGSGPVGSSGSSSTFAGLHQHERMGYQLHGAEVNGGLPAASSFSSAPGATYGGVSSHTPPVS
          GS.P.PLPP.S.PVGS...SSTF.GLHQHERMGYQLH.AEVNGGLPAAS.FS.AP......VSSH.PPVS
Retrocopy GSYPPPLPPSSCPVGSGRGSSTFGGLHQHERMGYQLHRAEVNGGLPAASTFSLAPWSW--SVSSHRPPVS

Parental  GADSLLGSRGTTAGSSGDALGKA-LASIYSPDHSSNNFSSSPSTPVGSPQGLAGTSQWPRAGAPGALSPS
          GA...LGSRGTTAGSS.DAL..A...SIYSPDHSSN.FSSS.ST.VG.PQGL.G.S.WP..G.PGALSPS
Retrocopy GANIFLGSRGTTAGSSWDALRQA<MSSIYSPDHSSNSFSSSSSTAVGYPQGLGGMSHWPGTGVPGALSPS

Parental  YDGGLHGLQSKIEDHLDEAIHVLRSHAVGTAGDMHTLLPGHGALA-SGFAGPMSL-GGRHAGLVGGGHPE
          YDG..HG.QSK.EDHL..AIHVL.SH.VGTAG...TLLPGH.ALA..GFAGPM.L..G.HAGLV.G.HPE
Retrocopy YDGDFHGVQSKTEDHLNKAIHVLCSHTVGTAGNGPTLLPGHRALA<LGFAGPMLL>WGQHAGLVRG*HPE

Parental  DGLAGSTSLMHNHAALPSQPGALPDLSRPPDSYSGQGRAG
          DG..GS.SLMH.H.AL.S.PGAL.DLS.PPDSYSG.G.AG
Retrocopy DGPVGSASLMHIHVALSS*PGALSDLSWPPDSYSGLGQAG

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	3.03 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	9.52 RPM
SRP007412_cerebellum	0.00 RPM	2.71 RPM
SRP007412_heart	0.00 RPM	3.12 RPM
SRP007412_kidney	0.00 RPM	5.63 RPM
SRP007412_liver	0.20 RPM	8.51 RPM
SRP007412_testis	0.04 RPM	22.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1194 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1194 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4123
Gorilla gorilla	retro_ggor_2770

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000071564	1 retrocopy	retro_hsap_4123,
Gorilla gorilla	ENSGGOG00000003667	1 retrocopy	retro_ggor_2770,
Macaca mulatta	ENSMMUG00000009017	1 retrocopy	retro_mmul_1194 ,
Nomascus leucogenys	ENSNLEG00000001742	1 retrocopy	retro_nleu_2472,