RetrogeneDB ID: retro_pabe_1381

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:30452782..30453699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SETD8
• Ensembl ID: ENSPPYG00000005085
• Aliases: None
• Description: SET domain containing (lysine methyltransferase) 8 [Source:HGNC Symbol;Acc:29489]

Sequence

>retro_pabe_1381
GAGAATGTATTCACCGGGCAATCAAAGATCTATTCCTACCTGAGCCCCAACAAATGCTCTGGAAAGCGTTTCCCGTTTCA
GGAAGAGAGCTCAGTTACGCATCACGGAGTCAAATGCCAAGGAAACCATTAGCCGGAATCTCCAGGAAAAGAGAAGAGAA
AGGAAATGCAACAAGGAGCACCAGGAAGTCAGAGGAACAGAAGATCAAACATGCCAGGAGAAGTTCCCTGGCACCTTTTC
CAAACCAATAATCTGAAACAGCAGAACCTCCCAAAACTCTAACCTCGTTTTGTGATTCCACCAATGCAGCATCGCCAAGC
AAGCTCTGAGAAAGCCCTTCAAGGGCACAGAGCCCCGCCATCCCCCACTCCGGAAAAAAGCTCAAGGAAAAACGCAACAG
ACTCGCAAACTCTCGGATTTCTACCCTGTACGAAGCAGCTGCAGGAAGAGCAAAGGTGAGCTGCAGTCTGAAGAAAGGAA
AATAACAGATGATTTGATTGAAGATGGGAAGAAAGAAGGAATGAAGATTGACCTCGTTGATGGCAAAGGCAGGGATGCGA
TCGCCATCAAGCAGTTCTCCCAGAGTGACTTTGTGGTGAAATAACCACGAGGCCTCATCAAGACCGCGACGCCAAGATGC
AGGAGGCTTTTTACGCACAGGACCCTCCGTAAGCTGCTATATCTACCGTTTTCAGTATCTGAGCAAAACCTGCTGGATGC
AACTAGAGACACAAATCCCTTAGGAAGACTGATCAATCACAGCAAATGTGGGAATTGCCAAACCAAACTGCAGGACATCG
ACAGCTACCTTACGTCATCCTCATCGCCTCCCGAGACAGTGAGGCCTGGGAGGAGCTCCTGTATTACTGTGGGGACCGCC
CCAAGGCTCCCTGGAAGCCAACCGGTGCCTGAAGCAT

Alignment

ORF - retro_pabe_1381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.1 %
• Parental protein coverage: 99.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ENVFTGQSKIYSYMSPNKCSGMRFPLQEENSVAHHEVKCQG-KPLAGIYRKREEKRNAGNAVRSAMKSEE
          ENVFTGQSKIYSY.SPNKCSG.RFP.QEE.SV.HH.VKCQG.KPLAGI.RKREEK...GNA.RS..KSEE
Retrocopy ENVFTGQSKIYSYLSPNKCSGKRFPFQEESSVTHHGVKCQG<KPLAGISRKREEK---GNATRSTRKSEE

Parental  QKIKDARRGPLAPFPNQKSEAAEPPKTPPSSCDSTNAA-IAKQALKKPIKG---KQAPRKK-AQGKTQQN
          QKIK.ARR..LAPFPNQ.SE.AEPPKT..S.CDSTNAA.IAKQAL.KP.KG......P..K.AQGKTQQ.
Retrocopy QKIKHARRSSLAPFPNQ*SETAEPPKTLTSFCDSTNAA<IAKQALRKPFKGTEPRHPPLRKKAQGKTQQT

Parental  RKLTDFYPVRRSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGD
          RKL.DFYPVR.S.RKSK.ELQSEERK..D.LIE.GK.EGMKIDL.DGKGR..IA.KQFS..DFVV.....
Retrocopy RKLSDFYPVRSSCRKSKGELQSEERKITDDLIEDGKKEGMKIDLVDGKGRDAIAIKQFSQSDFVVK*PRG

Parental  LIEIT-DAKKREALYAQD-PSTGCYMYYFQYLSKTYC-VDATRETNRLGRLINHSKCGNCQTKLHDIDG-
          LI....DAK..EA.YAQD.PS..CY.Y.FQYLSKT.C..DATR.TN.LGRLINHSKCGNCQTKL.DID..
Retrocopy LIKTA<DAKMQEAFYAQD<PSVSCYIYRFQYLSKT-C<LDATRDTNPLGRLINHSKCGNCQTKLQDIDS<

Parental  VPHLILIASRDIAAGEELLYDYGDRSKA-SIEAHPWLKH
          .P..ILIASRD..A.EELLY..GDR.KA.S.EA...LKH
Retrocopy LPYVILIASRDSEAWEELLYYCGDRPKA<SLEANRCLKH

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	22.50 RPM
SRP007412_cerebellum	0.00 RPM	34.66 RPM
SRP007412_heart	0.00 RPM	14.06 RPM
SRP007412_kidney	0.00 RPM	35.30 RPM
SRP007412_liver	0.00 RPM	14.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1381 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1381 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1381 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294, retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381 ,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,