RetrogeneDB ID: retro_pabe_1210

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:108341464..108342319(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HOMER2
• Ensembl ID: ENSPPYG00000006735
• Aliases: None
• Description: homer homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:17513]

Sequence

>retro_pabe_1210
TGGAGCGGCGCCTGGGCTGAGCCAGGCCTCAGGGGCCTCCGCACGTGCCGCACGGGGAGCAGACGCCATGCAGGCGGAGA
CTGAGCGCGAGGAGAGGCCGGGTCGGAGTGGCCGCCGAAGCAGTGCCGGGGATGGAAGAACAGCCCATCTTCACCACCGG
AGCACAGGTCTTCCAGATTGACCCCAACACCAAAAAGAACTGGATGCCTGCGAGCAACAGGCGGCCACCATTTCCTGCTT
CTGTGATGTCACAAGGAACATCTATGGGATCGTCAGTGTGGACGGAGCCAAGGTGACCATAAACAGCACAATCACACCGA
ATATGACCTTCATCAACACGTCACAGACGTCTGGGCAGTGGGCCGACAGCAGAGCCAACACGGTGTTTGGTTTGGGGTTT
TCCTCTGAGCAGCAGCTGACAAAGTTTGCAGAGAAATTCCAGGAGGTGGAAGAAGCGGCCAAGACAGCCAAAGACAAGAC
CCAGGAGAACATGGAGCCCTCGAGTAATAATCCCGAGAATCCGGGCATGAAGCCCCATCTTCTACTCTGGCATCCAGTGT
CAACGGGACGGACGATGAAAGGCCTCTCAGGCCGCTGCAGCCGACACGCACCTGCAGTCTGAGAACCACAAGCTGAAGGC
GGCCTCGACGCAGAGAGCTGCCCACGGGAAGAGGTGGGAGATGGAGCTGCAGACCCGGCGGGAGAGCGACGCCCGGCTGC
CCGCGGCGCTGCAGGATTCGGTGGCCAGCGCGGAGCAGAGGAGGAGGCCGTGAGATCTACAGAGAGGAGAAGAACACGCA
GCTGAAGAGGAGGATCCAGGAGCTGGAGGCCGAGCTCCGAGAAAAGGAGACAGAG

Alignment

ORF - retro_pabe_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.07 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  WSGAGAEPGA-PGPPHVPRGERLPSGRRASAR-GPVGAAARAAPEMGEQPIFTTRAHVFQIDPNTKKNWM
          WSGA.AEPG...GPPHVP.GE..P..RR.SAR.G.VG.AA.A.P.M.EQPIFTT.A.VFQIDPNTKKNWM
Retrocopy WSGAWAEPGL<QGPPHVPHGEQTPCRRRLSARRGRVGVAAEAVPGMEEQPIFTTGAQVFQIDPNTKKNWM

Parental  PAS-KQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSEQ
          PAS..QA.T.S.F.DVTRN.Y.I.SVDGAKV.INSTITPNMTF..TSQ..GQWADSRANTVFGLGFSSEQ
Retrocopy PAS<QQAATISCFCDVTRNIYGIVSVDGAKVTINSTITPNMTFINTSQTSGQWADSRANTVFGLGFSSEQ

Parental  QLTKFAEKFQEVKEAAKIAKDKMQEKIETSSNH-SQESGRKTPSSTQASSVNGTDDE-KASHAGPANTHL
          QLTKFAEKFQEV.EAAK.AKDK.QE..E.SSN..S.ESG...PSST.ASSVNGTDDE.KAS.A..A.THL
Retrocopy QLTKFAEKFQEVEEAAKTAKDKTQENMEPSSNN<SRESGHEAPSSTLASSVNGTDDE<KASQAAAADTHL

Parental  KSENDKLKIALTQSAANVKKWEIELQTLRESNARLTTALQESAASVEQWKRQFSICRDE-NXXXXSKIDE
          .SEN.KLK.A.TQ.AA..K.WE.ELQT.RES.ARL..ALQ.S.AS.EQ..R.....R.E.N......I.E
Retrocopy QSENHKLKAASTQRAAHGKRWEMELQTRRESDARLPAALQDSVASAEQRRRP*DLQRGE>NTQLKRRIQE

Parental  LEEQCSEINRE
          LE....E...E
Retrocopy LEAELREKETE

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	7.74 RPM
SRP007412_cerebellum	0.00 RPM	9.12 RPM
SRP007412_heart	0.03 RPM	5.24 RPM
SRP007412_kidney	0.03 RPM	15.11 RPM
SRP007412_liver	0.00 RPM	4.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1210 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1210 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1468

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015884	3 retrocopies	retro_cjac_3556, retro_cjac_3614, retro_cjac_3871,
Cavia porcellus	ENSCPOG00000014688	1 retrocopy	retro_cpor_35,
Equus caballus	ENSECAG00000023619	3 retrocopies	retro_ecab_1046, retro_ecab_661, retro_ecab_692,
Homo sapiens	ENSG00000103942	1 retrocopy	retro_hsap_1468,
Macaca mulatta	ENSMMUG00000008297	1 retrocopy	retro_mmul_2278,
Nomascus leucogenys	ENSNLEG00000010953	1 retrocopy	retro_nleu_3002,
Pongo abelii	ENSPPYG00000006735	5 retrocopies	retro_pabe_1209, retro_pabe_1210 , retro_pabe_1217, retro_pabe_3566, retro_pabe_3568,