RetrogeneDB ID: retro_mmul_411

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:127468116..127468936(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000000502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM45A
• Ensembl ID: ENSMMUG00000008289
• Aliases: None
• Description: None

Sequence

>retro_mmul_411
AAGGTGACTCATTTTTCTGTTGTTCTGACCACCAGAGATTTTAACCCAGTGAAGTATGCTGCCTTCACTAGGATATTGTG
TAGAATGTACCCGAAACATGGGAGCCCAGTTAAAATGATGGAGAGTTATATTGCAGTTCTCACAAAGGGGATGTGCCAGA
GTAAAGAAAATGGCTCTTTCCTTAGTAAGGATTTTGATGTCCGAAAGGCCTACCTGGCTGGCTCCATCAGAGACATTGTA
TCTCAGTTTGGAATGGAAACTATTCTCTTACACACAGCACTGATGCTAAAGAAAAGAATTGTGGTGTATCACCCCAAAAT
AGAAGCGGTCCAGGAGTTTACCAGGACTCTGCCTGCCCTGGTGTGGCACCGACAGGACTGGACCATCCTTCACTCTTATG
TGCACCTCAACGCGGATGAGCTGGAAGCCCTGCAGATGTGCACAGGTTACATTGCTGGATTTGTAAACTTGGAGGAGAGC
AACAGACCAGACCTCTATGATGTGTTATTGAATCTGGCAGAGAGTGAGATTACCTTTGCTCCCCTTGCAAAAGAGGCCAT
GGCAATGGCCAAACTGCACAAAGAAATGGGTCAGCTAATTGTTCAGACTGCAGAAGATCCAGAGAAATCAGACAGCCAGG
TCATACAGGATATTGCTCTAAAAACGAGAAATCTTTACCAACCTACCACTGTTTTCAGAAGTTTCGGCTGATGGAGAAAA
GAGAGTCCTTAATTTGGAGGCGCTAAAGCAAAAATGATTTCCGCCAGCAACAGAAAACTTCCTTTATCATCTAGCAGCAG
CCGAACAAATGCTGAAAATC

Alignment

ORF - retro_mmul_411 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QVTHFSIVLTTKDFNPEKYAAFTRILCRMYLKHGSPVKMMESYIAVLTKGICQSEENGSFLSKDFDVRKA
          .VTHFS.VLTT.DFNP.KYAAFTRILCRMY.KHGSPVKMMESYIAVLTKG.CQS.ENGSFLSKDFDVRKA
Retrocopy KVTHFSVVLTTRDFNPVKYAAFTRILCRMYPKHGSPVKMMESYIAVLTKGMCQSKENGSFLSKDFDVRKA

Parental  YLAGSIKDIVSQFGMETVILHTALMLKKRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYMHLNADE
          YLAGSI.DIVSQFGMET..LHTALMLKKRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSY.HLNADE
Retrocopy YLAGSIRDIVSQFGMETILLHTALMLKKRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYVHLNADE

Parental  LEALQMCTGYIAGFVDLEVSNRPDLYDVFVNLAESEITIAPLAKEAMAMGKLHKEMGQLIVQSAEDPEKS
          LEALQMCTGYIAGFV.LE.SNRPDLYDV..NLAESEIT.APLAKEAMAM.KLHKEMGQLIVQ.AEDPEKS
Retrocopy LEALQMCTGYIAGFVNLEESNRPDLYDVLLNLAESEITFAPLAKEAMAMAKLHKEMGQLIVQTAEDPEKS

Parental  DSQVIQVTPSPSDLLETPVPL-SDFSADGEKRVLNLEALKQKRFPPATENFLYHLAAAEQMLKI
          DSQVIQ........L..P....S..SADGEKRVLNLEALKQK.FPPATENFLYHLAAAEQMLKI
Retrocopy DSQVIQDIALKTRNLYQPTTV>SEVSADGEKRVLNLEALKQK*FPPATENFLYHLAAAEQMLKI

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	0.78 RPM	10.76 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	11.34 RPM
SRP007412_cerebellum	0.65 RPM	8.91 RPM
SRP007412_heart	0.24 RPM	4.42 RPM
SRP007412_kidney	0.59 RPM	16.90 RPM
SRP007412_liver	0.40 RPM	11.64 RPM
SRP007412_testis	0.19 RPM	2.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_411 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_411 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_411 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000119979	1 retrocopy	retro_hsap_4757,
Macaca mulatta	ENSMMUG00000008289	1 retrocopy	retro_mmul_411 ,
Otolemur garnettii	ENSOGAG00000002070	2 retrocopies	retro_ogar_1298, retro_ogar_2990,
Vicugna pacos	ENSVPAG00000004890	1 retrocopy	retro_vpac_549,