RetrogeneDB ID: retro_mmul_2433

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:21848391..21849347(-)
• Located in intron of: ENSMMUG00000023648

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1864
• Ensembl ID: ENSMMUG00000010970
• Aliases: HNRNPR, HNRPR
• Description: None

Sequence

>retro_mmul_2433
TCACAAGCCAGATGCCGGCTGATGAGTGGAAAAGTAAAAGTATGGGGAAATGCAGTTACAGCTGAATGGACTGACCCTGT
GAAGAACCAGATCCAGAAGTCATAGCTAAGGTAAAAGTATTGTTTGTGAGAAATTTGGGCACAGACGAAATATTGGAAAA
GTCATTTTCTGAATTTGGAGAACTTCAAAGAGTAAATAAGTTGAAAGATTATGCATTTGTTCATTCTGAAGACAGAGGAG
CAGTCGTTAAGGCTATGGATGAAATGAATGGCAAAGAAATAGAAGGGGAAGAACTTGAAATAGTCTTAGCCAAGCCACCA
GACAAGAAAAGGAAAGAGCGCCAAGCTGCTAGACAGGCCTCCAGAAGCACTGCATATGAAGATTATCACTACACCCTCCT
CCTCGCATGCTGCCTCCGATGAGAGGTTGGGGGAGAGGTGGATATGGCTACCCTCCAGATCACTACGGCACGAAGATTAC
TATGGTTATTATTATCACAACTATCATGGAGGTTATGAAAACTCCCTACTATGGCTATGATGATGGCTATGCAGTAACAG
AAAGAGGAGGAAGGGGAGGGCAGGGTGCTCCACCACCACCAAGGGGGAGGGGAGCACCACCTCCAAGAGGTACAGCTGGC
TATTAACAAAGGGGGGCACCTTTGGGACCACCAAGAGGCTCTAGGGGTGGCAGAGGGGGTCCTGCACAACAGCAGAGAGG
CCGTGGCTGCGGTTCCCGTGGATCTTGGGGCAACCAGGAGGCAATGTAGGAGGCAAGAGAAGGCAGATGCTTACAACCAA
CCTGATTCCAAGCATCGTCAGACCAACCAGCAGAACTGGGTCTCTCAACCCATCGCTCAGCAGCCACTTCAGCAAGGTGG
TGACTATTCTGGTAACTATGGTTACAATAATGACAACCAGGAATTTTATCAGGATACTCATAGGTAACAGTGGAAG

Alignment

ORF - retro_mmul_2433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 52.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AQARRRLMSGKVKVWGNVVTVEWADPV-EEPDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVK
          .QAR.RLMSGKVKVWGN.VT.EW.DPV.EEPDPEV.AKVKVLFVRNL....T.EILEKSFSEFG.L.RV.
Retrocopy SQARCRLMSGKVKVWGNAVTAEWTDPV<EEPDPEVIAKVKVLFVRNLG---TDEILEKSFSEFGELQRVN

Parental  KLKDYAFVHFEDRGAAVKAMDEMNGKEIEGEEIEIVLAKPPDKKRKERQAARQASRSTAYEDYYY-HPPP
          KLKDYAFVH.EDRGA.VKAMDEMNGKEIEGEE.EIVLAKPPDKKRKERQAARQASRSTAYEDY.Y.HPPP
Retrocopy KLKDYAFVHSEDRGAVVKAMDEMNGKEIEGEELEIVLAKPPDKKRKERQAARQASRSTAYEDYHY<HPPP

Parental  RMPPPIRGRGRGGGRGGYGYPPDYYG-YEDYYDDYYGYDYHDYRGGYED-PYYGYDDGYAVRGRGGGRGG
          RM.PP.RG.GRGG....YGYPPD.YG..EDYY....GY.YH.Y.GGYE..PYYGYDDGYAV..R.GGRGG
Retrocopy RMLPPMRGWGRGG----YGYPPDHYG<HEDYY----GYYYHNYHGGYEN>PYYGYDDGYAVTER-GGRGG

Parental  RGAPPPPRGRGAPPPRGRAGYSQRGAPLGPPRGSRGGRGGPAQQQRGR--GSRGSRGNR-GGNVGGKR-K
          .GAPPPPRGRGAPPPRG.AGY.QRGAPLGPPRGSRGGRGGPAQQQRGR..GSRGS.GN..GGNVGGKR.K
Retrocopy QGAPPPPRGRGAPPPRGTAGY*QRGAPLGPPRGSRGGRGGPAQQQRGRGCGSRGSWGNQ<GGNVGGKR<K

Parental  ADGYNQPDSKRRQTNNQQNWGSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTYGQQWK
          AD.YNQPDSK.RQT.NQQNW.SQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDT...QWK
Retrocopy ADAYNQPDSKHRQT-NQQNWVSQPIAQQPLQQGGDYSGNYGYNNDNQEFYQDTHR*QWK

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	0.22 RPM	85.27 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	63.15 RPM
SRP007412_cerebellum	0.13 RPM	84.08 RPM
SRP007412_heart	0.06 RPM	51.58 RPM
SRP007412_kidney	0.12 RPM	48.83 RPM
SRP007412_liver	0.00 RPM	20.15 RPM
SRP007412_testis	0.90 RPM	52.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2433 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2433 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_651
Pan troglodytes	retro_ptro_474
Gorilla gorilla	retro_ggor_568

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125944	1 retrocopy	retro_hsap_651,
Gorilla gorilla	ENSGGOG00000013250	1 retrocopy	retro_ggor_568,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433 ,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843,
Monodelphis domestica	ENSMODG00000016144	1 retrocopy	retro_mdom_240,
Mus musculus	ENSMUSG00000066037	1 retrocopy	retro_mmus_458,
Otolemur garnettii	ENSOGAG00000009179	1 retrocopy	retro_ogar_3144,
Procavia capensis	ENSPCAG00000010462	1 retrocopy	retro_pcap_88,
Pan troglodytes	ENSPTRG00000000324	1 retrocopy	retro_ptro_474,
Tupaia belangeri	ENSTBEG00000002251	1 retrocopy	retro_tbel_4256,