RetrogeneDB ID: retro_pabe_2438

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:71639750..71640515(+)
• 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_2438
AAATTCACTAGAAGGGACCATTTGCTTGACGAAGCTAAAGGTCTTTTACCAGATGATGAGCTTACATTATTTTGTGAGAT
GAGTGTGGTACTAGATTCAGTAAACATATCAGGACATACTAATACAATTACTTTGAAGGTGGCTGAATGTCGACTAGGAG
AAGATTTATGTAATCTCTGTGAAAACACAAGATGTACAGACTGTAGTTTTTTGTGAGAGGGCAAGAATTTAAAGCTCATA
AATCTACTGGTACCTCCATCCCCAGTTTTTAATGCCATGTTTGAACATGAAATGGAAGAAAGCATAAAGAATCGAGTGGA
AATAAATGATTTAGACCCTGATGTTTTTAAAGAAATGATGAGATTCATTAACACAGGGAAATAACTAAACCTTGACAAAA
TGGCTGACAACTTGTTGGCAGCTGCAGACAAACATGCACTGGGAACAGCTGAAGGTCTTGTGTGAGGAAGCTTTGTGTAG
TAATCCCTCAGTAGAAAATGTTGTTGATACCCTTGTCCTTGCAGATTTGCACATTGCAGAACAGTTGAAAGCAAAAGCCA
TAGACATTATTAATAGGTGCATTGTACTTCAACCACTTGGGTGTAAAGAATAGAAAACAGAAACAGCAACCAAGCAACTG
ACGTAATGGAAACATCAAGGTGGAAGTCCATGATTCAGTCTCACCCTTACTTAGTAGCAGAAGCCTTCTGAGCACTAGCA
TCTGCACAGTGTCCACAGTTTGGCATTCCACACAAAATGGCTAAA

Alignment

ORF - retro_pabe_2438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 65.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGHTNTNTLKVPECRLAEDLGNLWENTRFTDCS-
          KF.RRD.LLDEA.GLLPDD.LTLFCE.SVV.DSVNISGHTNT.TLKV.ECRL.EDL.NL.ENTR.TDCS.
Retrocopy KFTRRDHLLDEAKGLLPDDELTLFCEMSVVLDSVNISGHTNTITLKVAECRLGEDLCNLCENTRCTDCS<

Parental  FFVRGQEFKAHKSVLAARSPVF-NAMFEHEMEESKKNRVEINDLDPEVFKEMMRFIYTGRAPNLDKMADN
          FFVRGQEFKAHKS......P.F.NAMFEHEMEES.KNRVEINDLDP.VFKEMMRFI.TG...NLDKMADN
Retrocopy FFVRGQEFKAHKST-GTSIPSF>NAMFEHEMEESIKNRVEINDLDPDVFKEMMRFINTGK*LNLDKMADN

Parental  LLAAADKYAL-ERLKVMCEEALCSNLSVENVADTLVLADLHSAEQLKAQAIDFINRCSVLRQLGCKDGK-
          LLAAADK.AL.E.LKV.CEEALCSN.SVENV.DTLVLADLH.AEQLKA.AID.INRC.VL..LGCK..K.
Retrocopy LLAAADKHAL>EQLKVLCEEALCSNPSVENVVDTLVLADLHIAEQLKAKAIDIINRCIVLQPLGCKE*K<

Parental  NWNSNQATDIMETSGWKSMIQSHPHLVAEAFRALASAQCPQFGIPRKRLK
          N.NSNQATD.METS.WKSMIQSHP.LVAEAF.ALASAQCPQFGIP.K..K
Retrocopy NRNSNQATDVMETSRWKSMIQSHPYLVAEAF*ALASAQCPQFGIPHKMAK

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	0.00 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_2438 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2438 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,