RetrogeneDB ID: retro_mmul_2278

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:169435541..169436144(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000017539
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HOMER2
• Ensembl ID: ENSMMUG00000008297
• Aliases: None
• Description: None

Sequence

>retro_mmul_2278
CGAGCACAGGTCTTCCCGATTGACCCCAACACCAAGAACTGGATGCCTGCAAGCAATAGGCGGTCACTGTTTCCTGCTTG
TATGATGTCACAAGGAAGAGCTATCGGATCGTCAGTGTGAACGGAGCCAAGGTGATCATAAACAGCACAATCACACCAAA
CACGACCTTCACCAACATGTCACAGAAGTCTGGGCAGTGGGCCGACAGCAAAGCCAACACGGTGTTTGGTTTGGGGTTTT
CCTCTGAGCAGCAGCCGACAAAGTTTGCAGAGAAATTCCAGGAGGTGGAAGAAGCGGCCAAGATAGCCAAAGACAAGAAC
CAGGAGAAAATGGAGCCCTCGAGTAATCAACCCTAAGAATCCTGGTGTGGATTCTTCTACTCTGGCATCCAGTGTCAACG
GGATGGACGATGAAAAGGCCTCGCATGCAGCTGCAGCCAACACGCACCTGCAGTACAGGAACAACAAGCTGAAGGCGGCC
TTGACGCAGGGCGCTGCCCACGGGAAGAGGCGAGAGATGGAGCTGCAGGCCTGGCGGGAGAGCGACGCCCGGCTGCCCAC
GGCGCTGCAGGAGTCCGCGGCCAGCGCGGAGCAGAGGAAGAGG

Alignment

ORF - retro_mmul_2278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RAHVFQIDPNTKKNWMPASKQ-AVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWA
          RA.VF.IDPNTK.NWMPAS...AVTVS..YDVTR.SYRI.SV.GAKVIINSTITPN.TFT..SQK.GQWA
Retrocopy RAQVFPIDPNTK-NWMPASNR<AVTVSCLYDVTRKSYRIVSVNGAKVIINSTITPNTTFTNMSQKSGQWA

Parental  DSRANTVFGLGFSSEQQLTKFAEKFQEVKEAAKIA-KDKTQEKIETSSDHSQESGRETPSSTQASSVNGT
          DS.ANTVFGLGFSSEQQ.TKFAEKFQEV.EAAKIA.K..T..K...........G....SST.ASSVNG.
Retrocopy DSKANTVFGLGFSSEQQPTKFAEKFQEVEEAAKIA>KTRTRRKWSPRVINPKNPGVD--SSTLASSVNGM

Parental  DDEKASHTGPANTHLKSENDKLKIALTQSAANVKKWEIELQTLRESNARLTTALQESAASVEQWKR
          DDEKASH...ANTHL...N.KLK.ALTQ.AA..K..E.ELQ..RES.ARL.TALQESAAS.EQ.KR
Retrocopy DDEKASHAAAANTHLQYRNNKLKAALTQGAAHGKRREMELQAWRESDARLPTALQESAASAEQRKR

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	10.98 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.58 RPM
SRP007412_cerebellum	0.00 RPM	12.14 RPM
SRP007412_heart	0.00 RPM	27.79 RPM
SRP007412_kidney	0.00 RPM	39.44 RPM
SRP007412_liver	0.00 RPM	31.07 RPM
SRP007412_testis	3.13 RPM	4.75 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2278 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2278 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015884	3 retrocopies	retro_cjac_3556, retro_cjac_3614, retro_cjac_3871,
Cavia porcellus	ENSCPOG00000014688	1 retrocopy	retro_cpor_35,
Equus caballus	ENSECAG00000023619	3 retrocopies	retro_ecab_1046, retro_ecab_661, retro_ecab_692,
Homo sapiens	ENSG00000103942	1 retrocopy	retro_hsap_1468,
Macaca mulatta	ENSMMUG00000008297	1 retrocopy	retro_mmul_2278 ,
Nomascus leucogenys	ENSNLEG00000010953	1 retrocopy	retro_nleu_3002,
Pongo abelii	ENSPPYG00000006735	5 retrocopies	retro_pabe_1209, retro_pabe_1210, retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,