RetrogeneDB ID: retro_pabe_3568

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:8121221..8121982(-)
• 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_3568
TGGAGCAGCGCCAGGGATGAGCCAGGCACGCAGGGGCCGCTGCATGTGACGTGCGAGGAGCGAAGCCCAGCAGGCCGAGA
GCCAGCGCGAGAGGCCGGGTCGGAAGCAGCCGCCAGAGCAGCATCAGAGATGGGAGAACAGCCCATCTTCACCACCCGAG
CGCGGGTCTTCCAGATTGACCCCAACACCAAGAACTGGATGCCTGCAAGCAACAAGCGGTCACCATTTCCTGCTTCTATG
ATGTTGCAAGTAACAGCTAGGGGATCATCAGTGTGGACAGAGCCAAGGTGACTATAAACAGCACAGTCACACTGAATATG
ACCTTCACCAACACGTCACAGCCGTCTGGGCAGTGGGCCGACAGCGAGCCAACACGGTGTTTGGTTTGGGGTTTTCCTCT
GAGCAGCTGCTGACAATGTTTGCAGAGAAATTCCAGGAGGTGGAAGAAGCGGCCAATACAGCCAAAGACAAGACCCAGGA
GAACATGGAGCCCTCGAGTAATCATCCTGAGAATCAGGGCGTGGAGCCCCATCTTCTACTCCGGCATCCAGTGTCAACGG
GACAGACGATGAAAGGCTTCTCAGGCCACTGCAGCCGACACGCACCTGCAGTCTGGGAACCACAAGCTGAAGGCAGCCTC
AACGCAGAGTGCTGCCGACGGGAAGAAGTGGGAGATGGAGCTGCAGACCCGGCGGGAGAGCGACGCCCGGCTGACCACGG
CGCTGCTGGGGTCGGAGGCCAGTGTGGAGCAGAGGAAGAGG

Alignment

ORF - retro_pabe_3568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.43 %
• Parental protein coverage: 64.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  WSGAGAEPGAPGPPHVPRGERLPSGR-RASARGPVG-AAARAAPEMGEQPIFTTRAHVFQIDPNTKKNWM
          WS.A..EPG..GP.HV...ER.P.GR.RASARG.VG.AAARAA.EMGEQPIFTTRA.VFQIDPNT.KNWM
Retrocopy WSSARDEPGTQGPLHVTCEERSPAGR<RASARGRVG>AAARAASEMGEQPIFTTRARVFQIDPNT-KNWM

Parental  PAS-KQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADS-RANTVFGLGFSSE
          PAS..QAVT.S.FYDV..NS..IISVD.AKV.INST.T.NMTFT.TSQ..GQWADS.RANTVFGLGFSSE
Retrocopy PAS<QQAVTISCFYDVASNS*GIISVDRAKVTINSTVTLNMTFTNTSQPSGQWADS<RANTVFGLGFSSE

Parental  QQLTKFAEKFQEVKEAAKIAKDKMQEKIETSSNHSQ-ESGRKTPSSTQASSVNGTDDE-KASHAGPANTH
          Q.LT.FAEKFQEV.EAA..AKDK.QE..E.SSNH...ESGR..PSST.ASSVNGTDDE.KAS.A..A.TH
Retrocopy QLLTMFAEKFQEVEEAANTAKDKTQENMEPSSNHPE<ESGRGAPSSTPASSVNGTDDE<KASQATAADTH

Parental  LKSENDKLKIALTQSAANVKKWEIELQTLRESNARLTTALQESAASVEQWKR
          L.S.N.KLK.A.TQSAA..KKWE.ELQT.RES.ARLTTAL..S.ASVEQ.KR
Retrocopy LQSGNHKLKAASTQSAADGKKWEMELQTRRESDARLTTALLGSEASVEQRKR

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	0.00 RPM	5.24 RPM
SRP007412_kidney	0.00 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_3568 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3568 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 ,