RetrogeneDB ID: retro_mmul_1000

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:100363405..100364604(+)
• 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_1000
ATGAATTACGTAGAGAAGTATGGCATGAAGTGCGAAGGCATCTATAGGGTATCAGGAATTAAATCAAAGGTGGATGAGCT
AAAAGCAGCCTATGACCAGGAGGAGTCTACAAACTGGGAAGAATATGAGCCTCACACTGTAGCCAGTTTGCAGAGGCAGT
ATTTGCGAGACCTTCCAGAGAATTTGCTTACCAAAGAGCTTATGCCCAGATTTGAAGAGGCTTGTGGGAGGACCACGGAG
ACTGAGAAAGTGCAGGAATTCCAGCGTTTACTCAAAGAACTGCCAGAAGGTAACTGTCTTCTGATTTCTTGGCTCATTGT
GCACAAGGGCCATCTCATCGCAAAGGAACTGGAAACAAAAATGAATATGCAGAACATTTCTGTAGTGCTCAGCCGAACTG
TGCAGATCAGCAATCTAGTCCTGTATGTGTTTTTCACACATGTGCAAGAACTCTTTGGAAATGTGGTACTAAACAAGTGA
CAAAACCTTGGCAATGGTCTAACATGGCCATGATGCCCACACTGCCAGAGACCCAGACAGGCAACGAGGAGGAGATCAGG
AGACAGGAGTTGCTTTTGAATTGTTTACATCAAGATCTGCAGGGTGGGATAAAGGATTTGTCTAAAGAAGAAAGATTATG
GGAAGTACAAAGAATTTTGACAGCTCTCAAAAGACAACTGAGAGAAGCTGAAAGACAGGAGTGTGAAACCAAGATTGCAC
AAGAGATAGCCCGTCTTTCAAAAGAGGCTGTTTCCAAAAAAGAAATGAATGAAAATGAAGAAGTTATAAATATTCTCCTT
GTTCAGGAGAAAGAGATCCTGACTGAACAGGAGGAGGTCCTGGCCATGGAGCAGTTTCTGTGCCAGCAGATTGCCTCAGA
AAAAGAAGAGATTGCAGAAATTCAGAGTCGCCAGCAGCAGGGCTTAAGCAAGACTGAGGAGTACTCCTCCAAGAGCGACA
GTGAGGATGAGGAGGAGCCGCAGATCACTCTGGAAGATTTACAGAGACAGAACGAAGAGGTGGAAATAAAGAACGATCAT
TTGAATCAAGCAATTCACAAGGAGCGTGAGGCCATCATCGAGCAGTTCCAGCTGCTCCAGATGCAGCCAGCCACGGCCGA
GCAGCAGGCGCAGGAGGACGAGGAGCCCGAGTGGCGCACAGGTGCTGTCGAGCCGCCCAGAGACGGCGTCCTCGAGCCG

Alignment

ORF - retro_mmul_1000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDYVEKYGMKCEGIYRVSGIKSKVDELKAAYDREESTNLEEYEPNTVASLLKQYLRDLPENLLTKELMPR
          ..YVEKYGMKCEGIYRVSGIKSKVDELKAAYD.EESTN.EEYEP.TVASL..QYLRDLPENLLTKELMPR
Retrocopy MNYVEKYGMKCEGIYRVSGIKSKVDELKAAYDQEESTNWEEYEPHTVASLQRQYLRDLPENLLTKELMPR

Parental  FEEACGRTTETEKVQEFQRLLKELPECNYLLISWLIVHMDHVIAKELETKMNIQNISIVLP-TVQISNRV
          FEEACGRTTETEKVQEFQRLLKELPE.N.LLISWLIVH..H.IAKELETKMN.QNIS.VL..TVQISN.V
Retrocopy FEEACGRTTETEKVQEFQRLLKELPEGNCLLISWLIVHKGHLIAKELETKMNMQNISVVLSRTVQISNLV

Parental  LYVFFTHVQELFGNVVL-KQVTKPLRWSNMATMPTLPETQAGIKEEIRRQEFLLNCLHRDLQGGIKDLSK
          LYVFFTHVQELFGNVVL.KQVTKP..WSNMA.MPTLPETQ.G..EEIRRQE.LLNCLH.DLQGGIKDLSK
Retrocopy LYVFFTHVQELFGNVVL<KQVTKPWQWSNMAMMPTLPETQTGNEEEIRRQELLLNCLHQDLQGGIKDLSK

Parental  EERLWEVQRILTALKRKLREAKRQECETKIAQEIASLSKEDVSKEEMNENEEVINILLAQENEILTEQEE
          EERLWEVQRILTALKR.LREA.RQECETKIAQEIA.LSKE.VSK.EMNENEEVINILL.QE.EILTEQEE
Retrocopy EERLWEVQRILTALKRQLREAERQECETKIAQEIARLSKEAVSKKEMNENEEVINILLVQEKEILTEQEE

Parental  LLAMEQFLRRQIASEKEEIERLRAEIAEIQSRQQHGRSETEEYSSESESESEDEEELQIILEDLQRQNEE
          .LAMEQFL..QIASEKEEI...........S......S.....S...E......E.LQ...E.....N..
Retrocopy VLAMEQFLCQQIASEKEEIAEIQSRQQQGLSKTEEYSSKSD--SEDEEEPQITLEDLQRQNEEVEIKNDH

Parental  LEIKNNHLNQAIHEEREAIIELRVQLRLLQMQRAKAEQQAQEDQEPEWRGGAVQP
          L.........AI.E...............Q.Q............EP..R.G...P
Retrocopy LNQAIHKEREAIIEQFQ-LLQMQPATAEQQAQEDEEPEWRTGAVEPP-RDGVLEP

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	55.24 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	88.85 RPM
SRP007412_cerebellum	0.26 RPM	44.10 RPM
SRP007412_heart	0.12 RPM	39.75 RPM
SRP007412_kidney	0.00 RPM	43.78 RPM
SRP007412_liver	0.00 RPM	16.86 RPM
SRP007412_testis	0.23 RPM	11.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1000 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1000 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1000 has 0 orthologous retrocopies within eutheria group .

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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,