RetrogeneDB ID: retro_pabe_2273

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:184019476..184020979(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALBP1
• Ensembl ID: ENSPPYG00000009010
• Aliases: None
• Description: ralA binding protein 1 [Source:HGNC Symbol;Acc:9841]

Sequence

>retro_pabe_2273
AAGTCAAAAGACTTGACAGCAGCTGATGTTGTTAAACAGTGGAAGGAAAAAGAAAAAGAAAAACCAATTCAGGAGCCAGA
GGTGCCTCAGATTGATGTTCCAAATCTCAAACCCATTTTTGGAATTCCTTTGGCTGATGCAGTAGAGAGGACCATAATGT
ATGATGGCATTCGGCTGCCGGCCGTTTTCTGTGAATGTATAGATCACTCAGAGAAGTATTGCATGAAATGCGAAGGCATC
TACAGAGTATCAGGAATTAAATCAAAGGTGGATGAGCTAAAAGCAGCCTAGACCGGGGGGAGTCTACCAACTTGGAAGAA
TATGAGCCTAACACTGTAGCCAGTTTGCTGAAGCAGTATTTGTGAGACCTTCCAGAGAATTTGGTTACCAAAGAGCTTAT
GCCAAGATTTGAAGAAGCCTGTGGGAGGACCACGGAGACTGAGAAAGTGCAGGAATTCCAGCGTTTACTCAAATAACTGC
CAGAATGTAACTATCTTCTGATTTCTTGGCTCATTGTGCACACGGACCATGTCATCGCAAATGAACTAGAAACAAAAATG
AATAAACAGAACATTTCTATAGTGCTCAGCCCAACTGTGCAGATCAGCAATCGAGTCCTGTATGTGTTTTTCACACAAGG
GCAAGAACTCTTTGGAAATGTGGTACTAAAGCAAGTGACGAAACCTCTGCGATGGTCTAACGTGGCCACAATGCCCATGC
TGCCAGAGACCCAGGCAGGCATCAAGGAGATCAGGAGACAGGGTATTCTTTTGAATTGTTTACATTGATATCTGCAGGGT
GGGATAAAGGATTTATCTAAAGAAGAAAGATTATGGAAAGTCCAAAGAATTTTGACAGCCCTCAAAAGAAAACTGAGAGA
AGCTTAAAGACAGGAGTGTGAAACCAAGATTGCACAAAAGATAGCCAGTCTTTTAAAAGAGGATGTTTCCAAAGAAGAGA
TGAATGAAAATGAAGAAGTTATAAATATTCTCCTTGCTCAGGAGAATGAGATCCTGACTGAACGGGAGGAGCTCCTGACC
ATGGAGCAGTTTCTACACTGGCAGATTTCCTCAGAAAAAGAAGAGATGGGATGCCTCAGAGCCGAGATTGCTGAAATTCA
GTCACCAGCAGCACGGCCGAAGTGAGACTGAGGAGTACTCCTCCGAGAGCGAGAGTGCGGATGAGGAGGAGCTGCAGATT
ATTCTGGAATGTTTACAGAGACAGAACGAAGAGCTGGAAATAAAGAACAATCATTTGAATCAAGCAGTTCAAGAGGAGCG
CGAGGTCATCACTGAGCTGCGCGTGCAGCTCCTGCTGCTCCATATGCAGGGAGCCAAGGCTGAGCAGCAGGTGCAGGAGG
ACCAGGAGCCTGAGTGGCGCGGGGGTGCCGTCCAGCCGCCCAGAGACTGTGTCCTCGGGCCAAAAGAAGCTAAAGAGCAG
CCAAAGGCAGGCAAAGAGCCGGTGAAGCCATCGCCCAGCAGGGACAGGAAGGAGACGTCCATC

Alignment

ORF - retro_pabe_2273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 77.25 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSKDLTAADVVKQWKEKKKKKKPIQEPEVPQIDVPNLKPIFGIPLADAVERTMMYDGIRLPAVFRECIDY
          KSKDLTAADVVKQWK.......PIQEPEVPQIDVPNLKPIFGIPLADAVERT.MYDGIRLPAVF.ECID.
Retrocopy KSKDLTAADVVKQWKXXXXXX-PIQEPEVPQIDVPNLKPIFGIPLADAVERTIMYDGIRLPAVFCECIDH

Parental  VEKYGMKCEGIYRVSGIKSKVDELKAA-YDREESTNLEDYEPNTVASLLKQYLRDLPENLLTKELMPRFE
          .EKY.MKCEGIYRVSGIKSKVDELKAA..DR.ESTNLE.YEPNTVASLLKQYL.DLPENL.TKELMPRFE
Retrocopy SEKYCMKCEGIYRVSGIKSKVDELKAA<LDRGESTNLEEYEPNTVASLLKQYL*DLPENLVTKELMPRFE

Parental  EACGRTTEAEKVQEFQRLLKELPECNYLLISWLIVHMDHVIAKELETKMNIQNISIVLSPTVQISNRVLY
          EACGRTTE.EKVQEFQRLLK.LPECNYLLISWLIVH.DHVIA.ELETKMN.QNISIVLSPTVQISNRVLY
Retrocopy EACGRTTETEKVQEFQRLLK*LPECNYLLISWLIVHTDHVIANELETKMNKQNISIVLSPTVQISNRVLY

Parental  VFFTHVQELFGNVVLKQVMKPLRWSNMATMPTLPETQAGIKEEIRRQEFLLNCLHRDLQGGIKDLSKEER
          VFFT..QELFGNVVLKQV.KPLRWSN.ATMP.LPETQAGIK.EIRRQ..LLNCLH..LQGGIKDLSKEER
Retrocopy VFFTQGQELFGNVVLKQVTKPLRWSNVATMPMLPETQAGIK-EIRRQGILLNCLH*YLQGGIKDLSKEER

Parental  LWEVQRILTALKRKLREAKRQECETKIAQEIASLSKEDVSKEEMNENEEVINILLAQENEILTEQEELLA
          LW.VQRILTALKRKLREA.RQECETKIAQ.IASL.KEDVSKEEMNENEEVINILLAQENEILTE.EELL.
Retrocopy LWKVQRILTALKRKLREA*RQECETKIAQKIASLLKEDVSKEEMNENEEVINILLAQENEILTEREELLT

Parental  MEQFLRRQIASEKEEIERLRAEIAEIQS-RQQHGRSETEEYSSESESESEDEEELQIILEDLQRQNEELE
          MEQFL..QI.SEKEE...LRAEIAEIQS..Q.......E..S.......E...ELQIILE.LQRQNEELE
Retrocopy MEQFLHWQISSEKEEMGCLRAEIAEIQS>QQHGRSETEEYSSESESADEE---ELQIILECLQRQNEELE

Parental  IKNNHLNQAIHEEREAIIELRVQLRLLQMQRAKAEQQAQEDEEPEWRGGAVQPPRDGVLEPKAAKEQPKA
          IKNNHLNQA..EERE.I.ELRVQL.LL.MQ.AKAEQQ.QED.EPEWRGGAVQPPRD.VL.PK.AKEQPKA
Retrocopy IKNNHLNQAVQEEREVITELRVQLLLLHMQGAKAEQQVQEDQEPEWRGGAVQPPRDCVLGPKEAKEQPKA

Parental  GKEPAKPSPSRDRKETSI
          GKEP.KPSPSRDRKETSI
Retrocopy GKEPVKPSPSRDRKETSI

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	0.00 RPM	83.32 RPM
SRP007412_cerebellum	0.00 RPM	65.79 RPM
SRP007412_heart	0.00 RPM	42.57 RPM
SRP007412_kidney	0.00 RPM	62.61 RPM
SRP007412_liver	0.00 RPM	24.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2273 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2273 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
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,