RetrogeneDB ID: retro_pabe_919

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:44677749..44679297(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHA8
• Ensembl ID: ENSPPYG00000017682
• Aliases: None
• Description: pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8 [Source:HGNC Symbol;Acc:30037]

Sequence

>retro_pabe_919
ATGGAGGGGGTGCTGTACAAGTGGCCAAACTATCTGAGCAGTTGGCAGCCTCGATGGTTCCTTCTCTGTGGGGGAATATT
GTCCTATTATGATTCTCCTGAAGATGCCTGAAAAGGTTGCAAAGGGAGCATACAAATGGCAGTCTGTGAAATTCAACTTC
ATTCTGTAGATAATACATGCGTGGACCTGATAATCCCCAGGGAACAGTATTTCTACCTGAAGTCCAGAAGTGTGGCTGAA
AGATAGCAGTGGCTGGTGGCCCTGGGATCAGCCAAGGCTTGCCTGACTGACAGTAGGACCCAGAAGGAGAAAGAGTTTGC
TGAAAACTTGAAAACCAAAATGTCAGAATTAAGACTCTGCTGTGACCTCCTTGTTCAGCAAGTAGATAAAACAAAAGAAG
TGACCACAACTGGTGTGTCCAATTCTGAGGAGGGAATTGATGTGGGAACTTTGCTGAAATCAACCTGTAATACTTTTCTG
AAGACCTTGGAAGAATGCATGCAGATCGCAAATGCAGCCTTCACCTCCGAGCTGCTCTACCGCACTCCACCAGGATCACC
GCAGCTGGCCATGCTCAAGTCCAGCAAGATGAAACATCCTATTATACCAATTCGTAATTCATTGGAAAGGCAAATGGAGT
TGAGCACTTGTGAAAATGGATCTTTAAATATGGAAATAAATGGTGAGGAAGAAATCCTAATGAAAAATAAGAATTCCTTT
TATTTGAAATCTGCAGAGATAGACTGCAGCACATCAAGTGAGGAAAATACAGATGATAATGTAACAGTCCAAGGTGAAAT
AATGAAGGAAGATGGAATGGAAAACCTGAAAAATCTTGACAGTAACTCGACTCAGTCTGGATCAGACTCAAGTTGCTCTC
CAGAATGCCTCTGGGAGGAAGGCAAAGAAGTTATCCCAACTTTCTTTAGTACCATGAACACAAGCTTTAGTGACATTGAA
CTTCTGGAAGACAGTGGCATTCCCGCAGAAGCATTCTTGGCATCATGCTATGCTGTGGTTCCAGTATTAGACAAACTTGG
CCCTACAGTGTTTGCTCCTGTTAAGATGGATCTTGTTGGAAATATTAAGAAAGTAAATCAGAAGTATATAACCAACAAAG
AAGAGTTTACCACTCTCCAGAAGATAGTGCTGCACGAAGTGGAGGTGGATGTAGCCCAGGTTAGGAACTCAGCGACTGAA
GCCCTCTTGTGGCTGAAGAGAGGTCTCAAATTTTTGAAGGGATTTTTGACAGAAGTGAAAAATGGGGAAAAGGATATCCA
GACAGCCCTGAATAACGCATATGGTAAAACATTGCGGCAACACAATGGCTGGGTATTTCGAGTGGTTTTTGCGTTAGCTT
TAAGGTCAACTCTATCCTATGAAGATTTTGTGGCTGTGTTAACCATAAAGGAAGGTGACCACCAGAAAGAAGCTTTCAGT
ATTGGGATGCAGAGGGACCTCAGCCTTTACCTCCCTGCCATGGAGAAGCAGCTGGCCATACTGGACGCTTTAGAAGAGGT
CCACAGGCTGGAATCTGATGAGGTGGTA

Alignment

ORF - retro_pabe_919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGVLYKWTNYLSGWQPRWFLLCGGILSYYDSPEDAWKGCKGSIQMAVCEIQVHSVDNTRMDLIIPGEQY
          MEGVLYKW.NYLS.WQPRWFLLCGGILSYYDSPEDA.KGCKGSIQMAVCEIQ.HSVDNT..DLIIP.EQY
Retrocopy MEGVLYKWPNYLSSWQPRWFLLCGGILSYYDSPEDA*KGCKGSIQMAVCEIQLHSVDNTCVDLIIPREQY

Parental  FYLKARSVAERQRWLVALGSAKACLTDSRTQKEKEFAENTENLKTKMSELRLYCDLLVQQVDKTKEVTTT
          FYLK.RSVAER..WLVALGSAKACLTDSRTQKEKEFA...ENLKTKMSELRL.CDLLVQQVDKTKEVTTT
Retrocopy FYLKSRSVAER*QWLVALGSAKACLTDSRTQKEKEFA---ENLKTKMSELRLCCDLLVQQVDKTKEVTTT

Parental  GVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPIHNS
          GVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPI.NS
Retrocopy GVSNSEEGIDVGTLLKSTCNTFLKTLEECMQIANAAFTSELLYRTPPGSPQLAMLKSSKMKHPIIPIRNS

Parental  LERQMELSTCENGSLNMEINGEEEILMKNKNSLYLKSAEIDCSISSEENTDDNITVQGEVMKEDGMENLK
          LERQMELSTCENGSLNMEINGEEEILMKNKNS.YLKSAEIDCS.SSEENTDDN.TVQGE.MKEDGMENLK
Retrocopy LERQMELSTCENGSLNMEINGEEEILMKNKNSFYLKSAEIDCSTSSEENTDDNVTVQGEIMKEDGMENLK

Parental  NHDNNLTQSGSDSSCSPEFLWEESKEVIPTFFSTMNTSFSDIELLEDSGIPTEAFLASCYAVVPVLDKLG
          N.D.N.TQSGSDSSCSPE.LWEE.KEVIPTFFSTMNTSFSDIELLEDSGIP.EAFLASCYAVVPVLDKLG
Retrocopy NLDSNSTQSGSDSSCSPECLWEEGKEVIPTFFSTMNTSFSDIELLEDSGIPAEAFLASCYAVVPVLDKLG

Parental  PTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEADVAQVRNSATEALLWLKRGLKFLKGFLT
          PTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVE.DVAQVRNSATEALLWLKRGLKFLKGFLT
Retrocopy PTVFAPVKMDLVGNIKKVNQKYITNKEEFTTLQKIVLHEVEVDVAQVRNSATEALLWLKRGLKFLKGFLT

Parental  EVKNGEKDIQTALNNAYGKTLRQHHGWVVRGVFALALRAAPSYEDFVAALTIKEGDHQKEAFSTGMQRDL
          EVKNGEKDIQTALNNAYGKTLRQH.GWV.R.VFALALR...SYEDFVA.LTIKEGDHQKEAFS.GMQRDL
Retrocopy EVKNGEKDIQTALNNAYGKTLRQHNGWVFRVVFALALRSTLSYEDFVAVLTIKEGDHQKEAFSIGMQRDL

Parental  SLYLPAMEKQLAILDTLYEVHGLESDEVV
          SLYLPAMEKQLAILD.L.EVH.LESDEVV
Retrocopy SLYLPAMEKQLAILDALEEVHRLESDEVV

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	0.39 RPM	2.76 RPM
SRP007412_cerebellum	0.61 RPM	4.74 RPM
SRP007412_heart	1.81 RPM	1.08 RPM
SRP007412_kidney	2.09 RPM	5.10 RPM
SRP007412_liver	1.77 RPM	4.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_919 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_919 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_919 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1110
Pan troglodytes	retro_ptro_688

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000106086	1 retrocopy	retro_hsap_1110,
Gorilla gorilla	ENSGGOG00000006031	1 retrocopy	retro_ggor_868,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pongo abelii	ENSPPYG00000017682	1 retrocopy	retro_pabe_919 ,
Pan troglodytes	ENSPTRG00000019036	1 retrocopy	retro_ptro_688,