RetrogeneDB ID: retro_pabe_2439

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:71835679..71836852(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSPPYG00000012825
• Aliases: None
• Description: speckle-type POZ protein-like [Source:HGNC Symbol;Acc:27934]

Sequence

>retro_pabe_2439
ATGTCTCAGGAACCTGCCCCACCTCTACCTAGAGATAAGTCTTCTTGTCCAATAGTAGAAAACTAATATTATACACAGAT
CAAAATAGTAAAATGTTCAACACATAGACCATTAATAAGTTCAGTTTTTGTCAAGAGGAAATGGGTGAGGTGTTAAAAAG
TTCCACATTTTCACCTGGCCCAAATGACAAAGTGAAATGGGGCCTGAGGGTAAACCTAAAGGGATTAGGTAACGAAAGTA
AAGACTACTTGGTCCTTAAATTTGCTTTTAGTCAGATGCCCCAAAAGTGAAGTGTGAGCAAAATTCAAATTTTCCCTTCT
GAATGCTAAAAGGGAAGAAACAAAAGCAATGGAAAGCCAAAGAACATATCAATTTGTGCAAGGGAAGGACTGGGATTTTT
AAAAATTCATTAGAAGAGACCTTTTGCTTGACAAAGCTAATAGTCTTTTACCAGATGACAAGCTTACATTATTTTATGAG
ATGAGTGTGATCCAAGATTCAGTAAACAAATCAGGACATACTAATACAAATACTTTGAAGGTGGCTGAGGGTCGACTAGG
AGAAGATTGAGGTAATCTCTGGGAAAACACAAGATTTATAGACTGCAGTTTTTAGTGAGAGGACAAGAATTTAAAGCTCA
TAAATCTGCTTGTACCTCAATCCCTAGTTTTTAATGCCATGTTTGAACATGAAATGGAAGAAAGCATAAAGAATTGAGTG
GAAATAAATGATTTAGACCCTGATGTTTTAAAGAAATGGTGAGATTCCTTAACACAGTGAAAGGATTAAACCTTGACAAA
ATGGCTGACAACTTGTTGGCAGCTGCAGACAAACATGCACTGGGAACAGCTGAAGGTCTTGTGTGAGGAAGCTTTGTGTA
GTAATCCCTCAGTAGAAAATGTTGCTGATACCTTTGTCCTTGAAGATTTGCACGTTGCAAAACAGTTGAAAGCACAAGCC
ACAGAAATTATTAATAGGTACATTGTACTTCAACAACTTGGGTGTAAGGATTAGAAAAACTGAAACAACAACCAAGCAAC
CAATGTAATGGAAACATCAAGGTGGAAGTCCATGATTCAGTCTCACCCTTACTTAGCAGCAGAAGCCTTCTGAGCACTAG
CATCTGCACAGTGTCCACAGTTTGGCATTCCACACAAACGGCTAAAACAGTCC

Alignment

ORF - retro_pabe_2439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 9
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MSREPTPPLPGDMSTGPIAESWCYTQVKVV-KFSYMWTINNFSFCREEMGEVLKSSTFSSGPSDKMKWCL
          MS.EP.PPLP.D.S..PI.E...YTQ.K.V.K.....TIN.FSFC.EEMGEVLKSSTFS.GP.DK.KW.L
Retrocopy MSQEPAPPLPRDKSSCPIVEN*YYTQIKIV<KMFNT*TINKFSFCQEEMGEVLKSSTFSPGPNDKVKWGL

Parental  RVNPKGLDDESKDYL-SLYLLLVSCPKSEVRAKFKFSLLNAKREETKAMESQRAYRFVQGKDWGFKKFIR
          RVN.KGL..ESKDYL.SL.LLLV.CPKSEV.AKFKFSLLNAKREETKAMESQR.Y.FVQGKDW.F.KFIR
Retrocopy RVNLKGLGNESKDYL>SLNLLLVRCPKSEV*AKFKFSLLNAKREETKAMESQRTYQFVQGKDWDF*KFIR

Parental  RDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCS-FFVR
          RD.LLD.AN.LLPDDKLTLF.E.SV.QDSVN.SGHTNTNTLKV.E.RL.ED.GNLWENTRF.DCS.F.VR
Retrocopy RDLLLDKANSLLPDDKLTLFYEMSVIQDSVNKSGHTNTNTLKVAEGRLGED*GNLWENTRFIDCS<FLVR

Parental  GQEFKAHKSVLAARSPVF-NAMFEHEMEESKKNRVEINDLDPEV-FKEMMRFIYTGRAPNLDKMADNLLA
          GQEFKAHKS......P.F.NAMFEHEMEES.KN.VEINDLDP.V.FKEM.RF..T....NLDKMADNLLA
Retrocopy GQEFKAHKSACTS-IPSF>NAMFEHEMEESIKN*VEINDLDPDV<FKEMVRFLNTVKGLNLDKMADNLLA

Parental  AADKYAL-ERLKVMCEEALCSNLSVENVADTLVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGKNWNS
          AADK.AL.E.LKV.CEEALCSN.SVENVADT.VL.DLH.A.QLKAQA...INR..VL.QLGCKD.KN.N.
Retrocopy AADKHAL>EQLKVLCEEALCSNPSVENVADTFVLEDLHVAKQLKAQATEIINRYIVLQQLGCKD*KN*NN

Parental  NQATDIMETSGWKSMIQSHPHLVAEAFRALASAQCPQFGIPRKRLKQS
          NQAT..METS.WKSMIQSHP.L.AEAF.ALASAQCPQFGIP.KRLKQS
Retrocopy NQATNVMETSRWKSMIQSHPYLAAEAF*ALASAQCPQFGIPHKRLKQS

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	12.00 RPM
SRP007412_cerebellum	0.00 RPM	22.74 RPM
SRP007412_heart	0.00 RPM	7.29 RPM
SRP007412_kidney	0.03 RPM	13.39 RPM
SRP007412_liver	0.00 RPM	7.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2439 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439 , retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,