RetrogeneDB ID: retro_pabe_1209

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:108101194..108102092(-)
• Located in intron of: ENSPPYG00000029895

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_1209
TGGGGCGGCGCCAGGGCTGAGCCGGGCGCGCAGGGGCCGCCGCATGTGCCCCGCGGGGAGCGGATGCCCAGCGGGCGTAG
AGCCAGCGCCAGAGGCCGGGTCGGAGTGGCCGCCGGAGCAGCGTCAGAGATGGGAGAACAGCCCATCTTCACCCCCAGAG
CGCGGGTCTTCCAGACTGACCCCAACACCAAGAAGAACTGGATGCCTGCAAGCAACAGGCGGCCACCATTTCCTGCTTCT
ATGATGTCACAAGGAACATCTATGGGATCGTCAGTGTGGACGGAGCCAAGGTGACCATAAACAACACAGTCACACCGATT
ATGACCTTCACCAACACGTCACAGACGTCTGGGCAGTGGGCCGACAGCAGAGCCTGCACGGTGTTTGGTTTGGAGTTTTT
CTCTGAGCAGCAGCTGACAAAGTTTGCAGATAAATTCCAGGAGGTGGAAGAAGCGGCCAATATAGCCAAAGACAAGAACC
AGGAGAACATGGAGCCCTCGAGTAATCATTCCCGAGAATCCGGGCATGAAGCCCCATCTTCTACTCCGGCAACCAGTGTC
AACGGGACGGACGACGGAAAGGCCTCTCAGGCCGCTGCAGCCGACACGCACCTGCAGTCTGGGAACCACAAGCTGAAGAC
GGCCTCAACGCAGAGCGCTGCCCGCGGGAAGAGGTGGGAGATGGAGCTGCAGACCCGGCGGGAGAGCGACTTCCGGCTGT
CCATGGCGCTGTAGGAGTCGACGGCCAGTGCGGAGCAGAGGAAGAGGCCGTCAGACAGAGTGCGACTGTGTCTCTGAGAA
GATGGAGGCGGCAGAGAGAGGATCAAAACCTGGAAGATAAAGTGCGTTCCCTAAAGCTAGGCCCTGAGGAGAGCAAATCC
CGACAGCGCCACCTGGAG

Alignment

ORF - retro_pabe_1209 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.23 %
• Parental protein coverage: 74.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WSGAGAEPGAPGPPHVPRGERLPSGRRASARGPVGAAARAAPEMGEQPIFTTRAHVFQIDPNTKKNWMPA
          W.GA.AEPGA.GPPHVPRGER.PSGRRASARG.VG.AA.AA.EMGEQPIFT.RA.VFQ.DPNTKKNWMPA
Retrocopy WGGARAEPGAQGPPHVPRGERMPSGRRASARGRVGVAAGAASEMGEQPIFTPRARVFQTDPNTKKNWMPA

Parental  S-KQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSEQQL
          S..QA.T.S.FYDVTRN.Y.I.SVDGAKV.IN.T.TP.MTFT.TSQ..GQWADSRA.TVFGL.F.SEQQL
Retrocopy S<QQAATISCFYDVTRNIYGIVSVDGAKVTINNTVTPIMTFTNTSQTSGQWADSRACTVFGLEFFSEQQL

Parental  TKFAEKFQEVKEAAKIAKDKMQEKIETSSNHSQESGRKTPSSTQASSVNGTDDEKASHAGPANTHLKSEN
          TKFA.KFQEV.EAA.IAKDK.QE..E.SSNHS.ESG...PSST.A.SVNGTDD.KAS.A..A.THL.S.N
Retrocopy TKFADKFQEVEEAANIAKDKNQENMEPSSNHSRESGHEAPSSTPATSVNGTDDGKASQAAAADTHLQSGN

Parental  DKLKIALTQSAANVKKWEIELQTLRESNARLTTALQESAASVEQWKR---QFSICRDENXXXXSKI-DEL
          .KLK.A.TQSAA..K.WE.ELQT.RES..RL..AL.ES.AS.EQ.KR.......C..E.......I...L
Retrocopy HKLKTASTQSAARGKRWEMELQTRRESDFRLSMAL*ESTASAEQRKRPSDRVRLCL*EDGGGRERI<QNL

Parental  EEQCSEINREKEKNTQLKRRIE
          E..........E......R..E
Retrocopy EDKVRSLKLGPEESKSRQRHLE

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	0.06 RPM	7.74 RPM
SRP007412_cerebellum	0.00 RPM	9.12 RPM
SRP007412_heart	0.03 RPM	5.24 RPM
SRP007412_kidney	0.00 RPM	15.11 RPM
SRP007412_liver	1.71 RPM	4.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1209 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1209 has 0 orthologous retrocopies within eutheria group .

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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,