RetrogeneDB ID: retro_mmul_1985

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:156413946..156414386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.14262
• Ensembl ID: ENSMMUG00000022717
• Aliases: None
• Description: acidic leucine-rich nuclear phosphoprotein 32 family member A [Source:RefSeq peptide;Acc:NP_001247747]

Sequence

>retro_mmul_1985
GTGAAATAACTTGTCCTGGACAGCAGTCGGTCGAATGCAGGCAAACTCGAAGGCCTCACAGATGACTTTGAAGAACTGGA
ATCTTAAGTACAATCAACGTAGGCCTCGCCTCAATCTCAAACTTACCAAAGTTAAACTAACTTAAGAAGCTTGAACTAAG
AGTCTCGGGGGGCCTGGAAGTATTGGCAGAAAAGTGTCCAAACCTCACATATCTAAATTTAAGTGGCAACAAAATTAAAG
ACCTCAGCACAATAGAGCCACTGAAAAAGTTAGAAAACCTCAAGAGCTTAGACCTTTTCAATTGCGAGGTAACCAACCTG
AACGATTCCCGAGAAAACGTGTTCAAGCTCCTCTCACAACTCACATATCTCCACGGCTATGACCGGGACGACAAGGAGGC
CCCTGACTCGGATGCTGAGGGCTACGTGGAAGGCCTGGAT

Alignment

ORF - retro_mmul_1985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.4 %
• Parental protein coverage: 78.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKELVLDNSRSNEGKLEGLTDEFEELE-FLSTINVGLTSIANLPKLNKLKKLELSDNRVSGGLEVLAEKC
          VK.LVLD.SRSN.GKLEGLTD.FEELE..LSTINVGL.SI.NLPKLN.LKKLEL...RVSGGLEVLAEKC
Retrocopy VK*LVLDSSRSNAGKLEGLTDDFEELE<ILSTINVGLASISNLPKLN*LKKLEL---RVSGGLEVLAEKC

Parental  PNLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGYDRDDKEAPD
          PNLT.LNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLND.RENVFKLL.QLTYL.GYDRDDKEAPD
Retrocopy PNLTYLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDSRENVFKLLSQLTYLHGYDRDDKEAPD

Parental  SDAEGYVEGLD
          SDAEGYVEGLD
Retrocopy SDAEGYVEGLD

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	0.11 RPM	88.86 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	81.79 RPM
SRP007412_cerebellum	0.13 RPM	119.66 RPM
SRP007412_heart	0.00 RPM	86.68 RPM
SRP007412_kidney	0.00 RPM	78.75 RPM
SRP007412_liver	0.00 RPM	28.30 RPM
SRP007412_testis	0.00 RPM	14.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1985 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1985 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3117
Pan troglodytes	retro_ptro_2108
Pongo abelii	retro_pabe_2575

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Macaca mulatta	ENSMMUG00000022717	1 retrocopy	retro_mmul_1985 ,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,