RetrogeneDB ID: retro_pabe_1922

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:8098047..8099358(+)
• 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_1922
GTGAATTACGTAGAGAAGTATGGCATGAAGTGCGAAGGCATCTACAGAGCATCAGGAATTAAATCAAAGGTGGATGAGCT
AAAAGCAGCCTACGACCAGGAGGAGTCTACAAACTTGGAAGAATATGAGCCTAACACTGTAGCCAGTTTGTGGAAGCAGT
ATTTGCGAGACCTTCCAGAGAATTTGCTTACCAAAGAGCTTATGCCTAGATTTGAAGAGGCTTATGGGAGGACCACGGAG
ACTGAGAAAGTGCAGGAATTCCAGCGTTTACTCAAAGAACTGCCAGAAGGTAACTGTCTTCTGATTTCTTGGCTCATTGT
GCACATGGACCATGTCATCGCAAAGGAACTGGAAGCAAAAATGAACATACAGAACATTTATATAGTGCTCAGCCCAACTG
TGCAGTTCAGCAACCTAGTCCTGTATGTGTTCTTCACACATGTGCAAGAACTTTTTGGAAATGTGGTTCTAAAGCAAGTG
ACGAAACCTCGGCGATGGTCTAACATGGCCACAATGCCCACGCTGCCAGAGACCCAGGCAGGCATCAAGGAGGAGATCAG
GAGACAGGAGTTGCTTTTGAATTGTTTACATCAAGATCTGCAGGGTGGGATAAAGGATTTGTCTGAAGAAGAAAGATTAT
GGGAAGTACAAAGAATTTTGACAGCCCTCAAAAGAAAACTGAGAGAAGCTAAAAGACAAGGGTGTGAAACCAAGATTGCA
CAAGAGATAGCCAGTCTTTCGAAAGAGGCTGTTTCCAAAAACGAGATGAATGAAAATGAAGAAGTTATAAATATTCTCCT
TGTTCAGGAGAAAGAGATCCTGACTAAACAGGAGGAGCTCCTGGCCATGGAGCAGTTTCTGCGCCGGCAGATTGCCTCAG
AAAAAGAAGAGATTGAATGCCTCAGAGCCGAGATTGCGGAAATTCAGAGTCGCCAGCAGCAGGGCCTAAGCGAGACTGAG
GAGTACTCCTCCAAGAGCGAGAGTGAGGATGAGGAGGAGCTGCAGATCATTCTGGAAGATTTACAGAGACAGAACGAAGA
GCTGGAAATAAAGAACAACCATTTGAATCAAGCAATTCACTAGGAGAGTGAGGCCATCATCGAGCTGCGCATGCAGCTCT
GGCTGCTCCAGATGCAGCCAGACAAGGCCGAGCAGCAGGTGCAGGAGGCCAAGGAGCCCATGTGGCGCGGGGGTGCCATC
CAGCCACACAAGGATGGCATCCTCGAGCTAATAGCAGCTAAATAGCCACCAAAGGCAGGCAAGAAGCCAGCAAAGCCATC
GCCCAGCAGGGACGGGAAGGAGACGTCCATC

Alignment

ORF - retro_pabe_1922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.38 %
• Parental protein coverage: 67.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDYVEKYGMKCEGIYRVSGIKSKVDELKAAYDREESTNLEDYEPNTVASLLKQYLRDLPENLLTKELMPR
          ..YVEKYGMKCEGIYR.SGIKSKVDELKAAYD.EESTNLE.YEPNTVASL.KQYLRDLPENLLTKELMPR
Retrocopy VNYVEKYGMKCEGIYRASGIKSKVDELKAAYDQEESTNLEEYEPNTVASLWKQYLRDLPENLLTKELMPR

Parental  FEEACGRTTEAEKVQEFQRLLKELPECNYLLISWLIVHMDHVIAKELETKMNIQNISIVLSPTVQISNRV
          FEEA.GRTTE.EKVQEFQRLLKELPE.N.LLISWLIVHMDHVIAKELE.KMNIQNI.IVLSPTVQ.SN.V
Retrocopy FEEAYGRTTETEKVQEFQRLLKELPEGNCLLISWLIVHMDHVIAKELEAKMNIQNIYIVLSPTVQFSNLV

Parental  LYVFFTHVQELFGNVVLKQVMKPLRWSNMATMPTLPETQAGIKEEIRRQEFLLNCLHRDLQGGIKDLSKE
          LYVFFTHVQELFGNVVLKQV.KP.RWSNMATMPTLPETQAGIKEEIRRQE.LLNCLH.DLQGGIKDLS.E
Retrocopy LYVFFTHVQELFGNVVLKQVTKPRRWSNMATMPTLPETQAGIKEEIRRQELLLNCLHQDLQGGIKDLSEE

Parental  ERLWEVQRILTALKRKLREAKRQECETKIAQEIASLSKEDVSKEEMNENEEVINILLAQENEILTEQEEL
          ERLWEVQRILTALKRKLREAKRQ.CETKIAQEIASLSKE.VSK.EMNENEEVINILL.QE.EILT.QEEL
Retrocopy ERLWEVQRILTALKRKLREAKRQGCETKIAQEIASLSKEAVSKNEMNENEEVINILLVQEKEILTKQEEL

Parental  LAMEQFLRRQIASEKEEIERLRAEIAEIQSRQQHGRSETEEYSSESESESEDEEELQIILEDLQRQNEEL
          LAMEQFLRRQIASEKEEIE.LRAEIAEIQSRQQ.G.SETEEYS..S.SESEDEEELQIILEDLQRQNEEL
Retrocopy LAMEQFLRRQIASEKEEIECLRAEIAEIQSRQQQGLSETEEYS--SKSESEDEEELQIILEDLQRQNEEL

Parental  EIKNNHLNQAIHEEREAIIELRVQLRLLQMQRAKAEQQAQEDEEPEWRGGAVQPPRDGVLEPKAAKEQPK
          EIKNNHLNQAIH.E.EAIIELR.QL.LLQMQ..KAEQQ.QE..EP.WRGGA.QP..DG.LE..AAK..PK
Retrocopy EIKNNHLNQAIH*ESEAIIELRMQLWLLQMQPDKAEQQVQEAKEPMWRGGAIQPHKDGILELIAAK*PPK

Parental  AGKEPAKPSPSRDRKETSI
          AGK.PAKPSPSRD.KETSI
Retrocopy AGKKPAKPSPSRDGKETSI

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	0.06 RPM	42.57 RPM
SRP007412_kidney	0.03 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_1922 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1922 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2129
Pan troglodytes	retro_ptro_1558

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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,