RetrogeneDB ID: retro_ptro_1558

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:100699048..100700360(+)
• 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_1558
GTGAATTACGTAGAGAAGTATGGCATGAAGTGTGAAGGCATCTACAGAGTATCAGGAATTAAATCAAAGATGGATGAGCT
AAAAGCAGCCTATGACCAGGAGAAGTCTACAAACTTGGAAGAATATGACCCTAACACTGTAGCCAGTTTGCGGAAGCAGT
ATTTGTGAGATCTTCCGGAGAATTTGCTTACCAAAGAGCTTATGCCTAGATTTGAACAGGCTTATGGGAGGACCACAGAG
ACTGAGAAAGTGCAGGAATTCCAGCGTTTACTCAAAGAACTGCCAGAAGGTAACTATCTTCTGATTTCTTGGTTCGTTGT
GCACATGGACCATGTCATCACAAAGGAACTGGAAGCAAAAATGAATATACAGAACATTTATATAGTGGTCAGCCCAACTG
TGCAGATCAGCAATCTAGTCCTGTATGTGTTCTTCACACATGTGCAAGAACTCTTTGGAAATGTGGTTCTAAAGCAAGGG
ACGAAACCTCGGCGATGGTCTAACGTGGCCACGATGCCCACGCTGCCAGAGACCCAGGCAGGCTTCAAGGAGGAGATCAG
GAGACAGGAGTCGCTTTTGAATTGTTTACATCAAGATCTGCAGGGTGGGATAAAGGATTTGTCTGAAGAAGAAAGATTAT
GGGAAGTACAAAGAATTTTGACAGCTCTCAAAAGAAAACTGAGAGAAGCTAAAAGACAGGGGTGTGAAACCAAGATTGCA
CAAGAGATAGCCAGTCTTTCAAAAGAGGCTGTTTCCAAAAAAAAAGATGAATGAAAATGAAGAAGTTATAAATATTCTCC
TTGTTCAGGAGAAAGAGATCCTGACTAAACAGGAGGAGCTCCTGGGCATGGAGCAGTTTCTGCGCCGGCAGATTGCCTCA
GAAAAAGAAGAGATTGAATGCCTCAGAGCCGAGACTGCGGAAATTCAGAGTCACCAGCAGCAGGGCCTAAGCGAGACTGA
GGAGTACTCCTCCGAGAGCGAGAGTGAGGATGAGGAGGAGCTGCAGATCGTTCTGGAAGATTTACAGAGACAGAATGAAG
AGCTGGAAATAAATAACAACCATTTGAATCAAGCAATTCACGAGGAGAGTGAGGCCGTCATCGAGCCGCGCATGCAGCCC
TGGCTGCTCCAGATGCAGCCAGACAGGGCCAAGCAGCAGGCGCAGGAGGACGAGGAGCCCGAGTGGCGCGGGGGTGCCAT
CCAGCCGCCCAAGAATGGCATCCTCGAGCCAGTAGCAGCTAAATAGCCACCAAAGGCAGGCAAGAAGCCGGCAAAGCCAT
TGCCCAGCAGGCATAGGAAGGAGACGTCCATC

Alignment

ORF - retro_ptro_1558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDYVEKYGMKCEGIYRVSGIKSKVDELKAAYDREESTNLEDYEPNTVASLLKQYLRDLPENLLTKELMPR
          ..YVEKYGMKCEGIYRVSGIKSK.DELKAAYD.E.STNLE.Y.PNTVASL.KQYL.DLPENLLTKELMPR
Retrocopy VNYVEKYGMKCEGIYRVSGIKSKMDELKAAYDQEKSTNLEEYDPNTVASLRKQYL*DLPENLLTKELMPR

Parental  FEEACGRTTEIEKVQEFQRLLKELPECNYLLISWLIVHMDHVIAKELETKMNIQNISIVLSPTVQISNRV
          FE.A.GRTTE.EKVQEFQRLLKELPE.NYLLISW..VHMDHVI.KELE.KMNIQNI.IV.SPTVQISN.V
Retrocopy FEQAYGRTTETEKVQEFQRLLKELPEGNYLLISWFVVHMDHVITKELEAKMNIQNIYIVVSPTVQISNLV

Parental  LYVFFTHVQELFGNVVLKQVMKPLRWSNMATMPTLPETQAGIKEEIRRQEFLLNCLHRDLQGGIKDLSKE
          LYVFFTHVQELFGNVVLKQ..KP.RWSN.ATMPTLPETQAG.KEEIRRQE.LLNCLH.DLQGGIKDLS.E
Retrocopy LYVFFTHVQELFGNVVLKQGTKPRRWSNVATMPTLPETQAGFKEEIRRQESLLNCLHQDLQGGIKDLSEE

Parental  ERLWEVQRILTALKRKLREAKRQECETKIAQEIASLSKEDVS-KEEMNENEEVINILLAQENEILTEQEE
          ERLWEVQRILTALKRKLREAKRQ.CETKIAQEIASLSKE.VS....MNENEEVINILL.QE.EILT.QEE
Retrocopy ERLWEVQRILTALKRKLREAKRQGCETKIAQEIASLSKEAVS>XXXMNENEEVINILLVQEKEILTKQEE

Parental  LLAMEQFLRRQIASEKEEIERLRAEIAEIQSRQQHGRSETEEYSSESESESEDEEELQIILEDLQRQNEE
          LL.MEQFLRRQIASEKEEIE.LRAE.AEIQS.QQ.G.SETEEYS..SESESEDEEELQI.LEDLQRQNEE
Retrocopy LLGMEQFLRRQIASEKEEIECLRAETAEIQSHQQQGLSETEEYS--SESESEDEEELQIVLEDLQRQNEE

Parental  LEIKNNHLNQAIHEEREAIIELRVQLRLLQMQRAKAEQQAQEDEEPEWRGGAVQPPRDGVLEPKAAKEQP
          LEI.NNHLNQAIHEE.EA.IE.R.Q..LLQMQ...A.QQAQEDEEPEWRGGA.QPP..G.LEP.AAK..P
Retrocopy LEINNNHLNQAIHEESEAVIEPRMQPWLLQMQPDRAKQQAQEDEEPEWRGGAIQPPKNGILEPVAAK*PP

Parental  KAGKEPAKPSPSRDRKETSI
          KAGK.PAKP.PSR.RKETSI
Retrocopy KAGKKPAKPLPSRHRKETSI

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	0.02 RPM	71.69 RPM
SRP007412_cerebellum	0.00 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	0.11 RPM	47.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1558 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1558 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2129
Pongo abelii	retro_pabe_1922

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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,