RetrogeneDB ID: retro_mmul_1528

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:106436465..106437932(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALBP1
• Ensembl ID: ENSMMUG00000019521
• Aliases: None
• Description: None

Sequence

>retro_mmul_1528
CCAATTCAGGAGCCAGAGGTGCCTCCGATTGATGTTCCAAATCTCAAACCCATTTTTGGAATTCCTTTGGCTGATGCAAT
AGAGAGGACCATGATGTATGATGGCATTTGGCTGCTGGTCGTTTTCCGTGAATGTATAGATTGCTTAGAGATGTATGGCA
TGAAATGCGAAGGTATCTACAGAGTATCAGGAATTAAGTCAAAGGTGGATAAGCTAAAAGCAGCCTATGACCAGGAGGAG
TCTACCAGCTTGGAAGAATATGAGCCTAATACTGTAGCCAGTTTGCTGAAGCAGTATTTGTGAGAACTTCCAGAGAACTT
GCTTTACTAAAGAGCTTATGCTGAGATTTGAAGAAGCTTATAGGAGGACCACAGAGACTGAGAAAGTTCATGAATACCAG
CATTTATTCAAATAACTGCCAGAATGTAACTATCTTCTGATTTCTTGGCTCATTGTGCACATGGACCATGTCATCACAAA
TGAACTGGAAACAAAAATGAATATACAGAACATTTCTATAGTGCTCAGCCCAACTGTGCAGATCAGCAATGGAGTCCCAC
ATGTGTTTTTCACACATGTGCAAGAACTCTTTGGAAATGCTGTACTAAAGCAAGTGACAAAACCTCTGCGATGGTCTAAC
ATGGCCACAATGCCCATGCTGCCAGAGACCCAGGCAGGCATCAAGGAGGAGATGAGGAGACAGGGTTTTCTTTTGAATTG
TTTATATCAATATCTGCAGGGTGGGAAAAAGGATTTATCTAAAGAAGAAAGATTATGGAAAGTCCAAAGAATTTTGACAG
CTCTCAAAAGAAAACTGAGAGAAATTTAAAGACAGGAGTGTGAAACCAAGATTGCACAAGAGATAGCCAGTCTTTGAAAA
GAGGGTGTTTCCAAAGAAGAGATGAACGAAAATTAAGAATTTATAAATATTCTCCTTGCTTGGGAGAATGAGATTCTGAC
TGAACAGGAGGAGCTCCTGACCATGGAGCAGTTTCTAGGCAGGCAGATTTCCTCAGAAAAAGAAGAGACATCTGAGGGAC
GCCTCAGAGTCGAGATTGCTGAAATTCAGAGTCGCCAGCAGCACGGCTGAAGTGAGACTGAGGAGTACTCCTCCGAGAGC
GAGAGATAGAGTGAGGATGAGGAGGAGCTGCAGATTATTCTGGAATATTTACAGAGACAGAACAAAGAGCTGGAAACAAA
GAACAATCATTTGAATCAAGCAATTCAAGAGGAGTGCGAGGTCATCATGGAGCTGCACGTGCAGCTCCAGCTGCTCCAGA
TGCAGGGACCCAAGGCTGAGCAGCAGGTGCAGGAGGACCAGGAGGACCAGGAGCCTAGGTGGCGCGGGGTGCTGTCCAGC
TGCCCAGAGATGGTGTCCTCTGGCCAAAAGAGGCTAAACGGCAGCCAAAGGCAGGCAAGGAGCTGGTGAAGCCATCACCC
AGCAGGGACAGGAGGGAGACGTCCATC

Alignment

ORF - retro_mmul_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.71 %
• Parental protein coverage: 73.85 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PIQEPEVPQIDVPNLKPIFGIPLADAVERTMMYDGIRLPAVFRECIDYVEKYGMKCEGIYRVSGIKSKVD
          PIQEPEVP.IDVPNLKPIFGIPLADA.ERTMMYDGI.L..VFRECID..E.YGMKCEGIYRVSGIKSKVD
Retrocopy PIQEPEVPPIDVPNLKPIFGIPLADAIERTMMYDGIWLLVVFRECIDCLEMYGMKCEGIYRVSGIKSKVD

Parental  ELKAAYDREESTNLEEYEPNTVASLLKQYLRDLPENLL-TKELMPRFEEACGRTTETEKVQEFQRLLKEL
          .LKAAYD.EEST.LEEYEPNTVASLLKQYL..LPENLL.TKELM.RFEEA..RTTETEKV.E.Q.L.K.L
Retrocopy KLKAAYDQEESTSLEEYEPNTVASLLKQYL*ELPENLL>TKELMLRFEEAYRRTTETEKVHEYQHLFK*L

Parental  PECNYLLISWLIVHMDHVIAKELETKMNIQNISIVL-PTVQISNRVLYVFFTHVQELFGNVVLKQVTKPL
          PECNYLLISWLIVHMDHVI..ELETKMNIQNISIVL.PTVQISN.V..VFFTHVQELFGN.VLKQVTKPL
Retrocopy PECNYLLISWLIVHMDHVITNELETKMNIQNISIVLSPTVQISNGVPHVFFTHVQELFGNAVLKQVTKPL

Parental  RWSNMATMPTLPETQAGIKEEIRRQEFLLNCLHRDLQGGIKDLSKEERLWEVQRILTALKRKLREAKRQE
          RWSNMATMP.LPETQAGIKEE.RRQ.FLLNCL...LQGG.KDLSKEERLW.VQRILTALKRKLRE..RQE
Retrocopy RWSNMATMPMLPETQAGIKEEMRRQGFLLNCLYQYLQGGKKDLSKEERLWKVQRILTALKRKLREI*RQE

Parental  CETKIAQEIASLSKEDVSKEEMNENEEVINILLAQENEILTEQEELLAMEQFLRRQIASEKEEIE--RLR
          CETKIAQEIASL.KE.VSKEEMNEN.E.INILLA.ENEILTEQEELL.MEQFL.RQI.SEKEE....RLR
Retrocopy CETKIAQEIASL*KEGVSKEEMNEN*EFINILLAWENEILTEQEELLTMEQFLGRQISSEKEETSEGRLR

Parental  AEIAEIQSRQQHGRSETEEYSSESESESEDEEELQIILEDLQRQNEELEIKNNHLNQAIHEEREAIIELR
          .EIAEIQSRQQHG.SETEEYSSESE..SEDEEELQIILE.LQRQN.ELE.KNNHLNQAI.EE.E.I.EL.
Retrocopy VEIAEIQSRQQHG*SETEEYSSESER*SEDEEELQIILEYLQRQNKELETKNNHLNQAIQEECEVIMELH

Parental  VQLRLLQMQRAKAEQQAQEDQE---PEWRG-GAVQPPRDGVLELKAAKEQPKAGKEPAKPSPSRDRKETS
          VQL.LLQMQ..KAEQQ.QEDQE...P.WRG.GAVQ.PRDGVL..K.AK.QPKAGKE..KPSPSRDR.ETS
Retrocopy VQLQLLQMQGPKAEQQVQEDQEDQEPRWRG<GAVQLPRDGVLWPKEAKRQPKAGKELVKPSPSRDRRETS

Parental  I
          I
Retrocopy I

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	55.24 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	88.85 RPM
SRP007412_cerebellum	0.26 RPM	44.10 RPM
SRP007412_heart	0.06 RPM	39.75 RPM
SRP007412_kidney	0.47 RPM	43.78 RPM
SRP007412_liver	0.00 RPM	16.86 RPM
SRP007412_testis	0.08 RPM	11.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1528 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1528 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2734
Pan troglodytes	retro_ptro_1848
Gorilla gorilla	retro_ggor_1903
Pongo abelii	retro_pabe_2273

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000017797	2 retrocopies	retro_hsap_2129, retro_hsap_2734,
Gorilla gorilla	ENSGGOG00000023120	1 retrocopy	retro_ggor_1903,
Macaca mulatta	ENSMMUG00000019521	2 retrocopies	retro_mmul_1000, retro_mmul_1528 ,
Nomascus leucogenys	ENSNLEG00000006950	1 retrocopy	retro_nleu_2532,
Pongo abelii	ENSPPYG00000009010	2 retrocopies	retro_pabe_1922, retro_pabe_2273,
Pan troglodytes	ENSPTRG00000009859	2 retrocopies	retro_ptro_1558, retro_ptro_1848,