RetrogeneDB ID: retro_mmul_522

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:118561586..118562113(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN12
• Ensembl ID: ENSMMUG00000023310
• Aliases: None
• Description: None

Sequence

>retro_mmul_522
TACTTTGGAAGTTTACTTGTCATTTTTTGTGCAGATCTGGCTAGTGGCATTTGGACATATGAAGAGAAGTGTATGATTCC
AGTACAGTGGTTAGATGTAGTCACTTTGAAAGTCAGAGTGGCAAATATGACTTACCTGGATACCAGTGGCTTACTCATGG
TTGGAAGGTTTTCAGTGGGAGTTTAAGTGTTGTGGAGTGGTATGTTTCAATGACTAGTTGGAAATGACAGAGACGGACTA
GCCCCCAGAATCCTGCTATGCTAGAGAATTCCCAGGATGTTCCAAACAAACCCACCAGGAAGATCTCAGTGACCTTTATC
AAGAGGATTGTGGTAAGAAAAATGTTTCCTTTTGAAAGGAACCAAACAATCACAGGCGCTAAGGTTTCTGGGAATTTCCA
TTAAAGTGACATAAACCTGGCCATGATTCTCACCACGACTTAGCTCTGGGCTCTGTATTATGAGAGAAGGGAGCCTGAGA
CAGACCAAATGATATTCCTGAAGCTCCTCTCAGCAACCCATGTCACT

Alignment

ORF - retro_mmul_522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.61 %
• Parental protein coverage: 58.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YFGSLLVIFCVELACGVWTYEQELMVPVQWSDMVTLKARMTN-YGLPRYRWLTHAWNFF-QREFKCCGVV
          YFGSLLVIFC..LA.G.WTYE...M.PVQW.D.VTLK.R..N.Y.LP.Y.WLTH.W..F.Q.EFKCCGVV
Retrocopy YFGSLLVIFCADLASGIWTYEEKCMIPVQWLDVVTLKVRVAN<YDLPGYQWLTHGWKVF<QWEFKCCGVV

Parental  YFTDWLEMTEMDWPPDSCCVREFPGCSKQAHQEDLSDLYQEGCGKKMYSF-LRGTKQLQVLRFLGISIGV
          .F.D.LEMTE.D.PP.SC..REFPGCSKQ.HQEDLSDLYQE.CGKK..SF.L.GTKQ.Q.LRFLGISI.V
Retrocopy CFND*LEMTETD*PPESCYAREFPGCSKQTHQEDLSDLYQEDCGKKNVSF<LKGTKQSQALRFLGISIKV

Parental  TQI-LAMILTITLLWALYYDRREPVTDQMMSLKNENSQHLS
          T...LAMILT.T.LWALYY.RREP.TDQM..LK.....H..
Retrocopy T*T<LAMILTTT*LWALYYERREPETDQMIFLKLLSATHVT

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	1.90 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.90 RPM
SRP007412_cerebellum	0.00 RPM	3.23 RPM
SRP007412_heart	0.00 RPM	18.61 RPM
SRP007412_kidney	0.00 RPM	22.89 RPM
SRP007412_liver	0.00 RPM	5.15 RPM
SRP007412_testis	0.00 RPM	2.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_522 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_522 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000023310	1 retrocopy	retro_mmul_522 ,