RetrogeneDB ID: retro_ptro_1848

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:184288169..184289610(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALBP1
• Ensembl ID: ENSPTRG00000009859
• Aliases: None
• Description: None

Sequence

>retro_ptro_1848
CCAATTCAGGAGCCAGAGGTGCCTCAGATTGATGTTCCAAATCTCAAACCCATTTTTGGAATTCCTTTGGCTGATGCAGT
AGAGAGGACCATGATGTATGATGGCATTCGGCTGCCGGCCATTTTCCGTGAATGTATAGATCACTTAGAGAAGTATGGCA
TGATGCGAAGGATCTACAGAGTATCAGGAATTAAATCAAAGGTGGATGAGCTAAAAGCAGCCTATGACCGGAAGGAGTCT
ACCAACTTGGAAGAATATGAGCCTAACACTGTAGCCAGTTTGCTGAAGCAGTATTTGTGAGACCTTCCAGAGAATTTGGT
TACCAAAGAGCTTATGCCGAGATTTGAAGAAGCTTGTGGGAGGACCACAGAGACTGAGAAAGTGCAGGAATTCCAGCGTT
TACTCAAAGAACTGCCAGAATGTAACTATCTTCTGATTTCTTGGCTCATTGTGCACATGGACCATGACATTGCAAATGAA
CTGGAAACAAAAATGAATAAACAGAACATTTCTATAGTGCTCAACCCAACTGTGCAGATCAGCAATTGAGTCCTGTATGT
GTTTTTCACACATGCGCAAGAACTCTCTGGAAATGTGGTACTAAAGCAAGTGACGAAACCTCTGCGATGGTCTAACATGG
CCACGATGCCCATGCTGCCAGAGACCCAGGCAAGGTATCAAGGAGGAGATCAGGAGACAGGGTTTTCTTTTGAATTGTTT
ACATCGATATCTGCAGTGTGGGATAAAGGATTTATCTAAAGAAGAAAGATTATGGAAAGTCCAAAGAATTTTGACAGCCC
TCAAAAGAAAACTGAGAGACGCTTAAAGACAGGAGTGTGAAACCAAGATTGCACAAAAGATAGCCAGTCTTTTAAAAGAG
GATGTTTCCAAAGAAGAGATGAATGAAAATGAAGAAGTTATAAATATTCTCCTTGCTTGGGAGAATGAGATCCTGACTGA
ATAGGAGGAGCTCCTGACCATGGAGCAGTTTCTACGCCAGCAGATTTCCTCAGAAAAAGAAGAGATGGGATGCCTCAGAG
CCGAGATTGCTGAAATTCAGAGTCACCAGCAGCACGGCCGAAGTGAGACTGAGGAGTACTCCTCTGAGAGCGAGAGTGAG
GATGAGGAGCTGCAGATTATTCTGGAATATTTACAGAGACAGCACGAAGAGCTGGAAATAAAGAACAATCATTTGAATCA
AGCAGTTCAAGAGGAGCGCGAGGTCATCATCGAGCTGCGCGTACAGTTCCGGCTGCTCCAGATGCAGGGACCCAAGGCTG
AGCAGCAGGTGCAGGAGGACCAGGAGCCTGAGTGGCGCGGTGGTGCCGTCCAGTCGCCCAGAGACTGTGTCCTCAGGCCA
AAAGAAGCTAAAGAGCAGCCAAAGGCAGGCAAAGAGCCGGTGAAGCCATCACCCAGCAGGGACAGGAAGGAGACGTCCAT
C

Alignment

ORF - retro_ptro_1848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.36 %
• Parental protein coverage: 73.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PIQEPEVPQIDVPNLKPIFGIPLADAVERTMMYDGIRLPAVFRECIDYVEKYGMKCEGIYRVSGIKSKVD
          PIQEPEVPQIDVPNLKPIFGIPLADAVERTMMYDGIRLPA.FRECID..EKYGM....IYRVSGIKSKVD
Retrocopy PIQEPEVPQIDVPNLKPIFGIPLADAVERTMMYDGIRLPAIFRECIDHLEKYGM-MRRIYRVSGIKSKVD

Parental  ELKAAYDREESTNLEDYEPNTVASLLKQYLRDLPENLLTKELMPRFEEACGRTTEIEKVQEFQRLLKELP
          ELKAAYDR.ESTNLE.YEPNTVASLLKQYL.DLPENL.TKELMPRFEEACGRTTE.EKVQEFQRLLKELP
Retrocopy ELKAAYDRKESTNLEEYEPNTVASLLKQYL*DLPENLVTKELMPRFEEACGRTTETEKVQEFQRLLKELP

Parental  ECNYLLISWLIVHMDHVIAKELETKMNIQNISIVLSPTVQISNRVLYVFFTHVQELFGNVVLKQVMKPLR
          ECNYLLISWLIVHMDH.IA.ELETKMN.QNISIVL.PTVQISN.VLYVFFTH.QEL.GNVVLKQV.KPLR
Retrocopy ECNYLLISWLIVHMDHDIANELETKMNKQNISIVLNPTVQISN*VLYVFFTHAQELSGNVVLKQVTKPLR

Parental  WSNMATMPTLPETQA-GIKEEIRRQEFLLNCLHRDLQGGIKDLSKEERLWEVQRILTALKRKLREAKRQE
          WSNMATMP.LPETQA.GIKEEIRRQ.FLLNCLHR.LQ.GIKDLSKEERLW.VQRILTALKRKLR.A.RQE
Retrocopy WSNMATMPMLPETQA>GIKEEIRRQGFLLNCLHRYLQCGIKDLSKEERLWKVQRILTALKRKLRDA*RQE

Parental  CETKIAQEIASLSKEDVSKEEMNENEEVINILLAQENEILTEQEELLAMEQFLRRQIASEKEEIERLRAE
          CETKIAQ.IASL.KEDVSKEEMNENEEVINILLA.ENEILTE.EELL.MEQFLR.QI.SEKEE...LRAE
Retrocopy CETKIAQKIASLLKEDVSKEEMNENEEVINILLAWENEILTE*EELLTMEQFLRQQISSEKEEMGCLRAE

Parental  IAEIQSRQQHGRSETEEYSSESESESEDEEELQIILEDLQRQNEELEIKNNHLNQAIHEEREAIIELRVQ
          IAEIQS.QQHGRSETEEYSSESESE....EELQIILE.LQRQ.EELEIKNNHLNQA..EERE.IIELRVQ
Retrocopy IAEIQSHQQHGRSETEEYSSESESE---DEELQIILEYLQRQHEELEIKNNHLNQAVQEEREVIIELRVQ

Parental  LRLLQMQRAKAEQQAQEDEEPEWRGGAVQPPRDGVLEPKAAKEQPKAGKEPAKPSPSRDRKETSI
          .RLLQMQ..KAEQQ.QED.EPEWRGGAVQ.PRD.VL................KPSPSRDRKETSI
Retrocopy FRLLQMQGPKAEQQVQEDQEPEWRGGAVQSPRDCVLXXXXXXXXXXXXXXXVKPSPSRDRKETSI

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_prefrontal_cortex	0.16 RPM	71.69 RPM
SRP007412_cerebellum	0.07 RPM	86.72 RPM
SRP007412_heart	0.00 RPM	60.25 RPM
SRP007412_kidney	0.00 RPM	73.12 RPM
SRP007412_liver	0.00 RPM	42.36 RPM
SRP007412_testis	0.00 RPM	47.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1848 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1848 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2734
Gorilla gorilla	retro_ggor_1903
Pongo abelii	retro_pabe_2273
Macaca mulatta	retro_mmul_1528

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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 ,