RetrogeneDB ID: retro_pabe_1476

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:5491784..5492278(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC9
• Ensembl ID: ENSPPYG00000015604
• Aliases: None
• Description: zinc finger CCHC domain-containing protein 9 [Source:RefSeq peptide;Acc:NP_001127522]

Sequence

>retro_pabe_1476
CTCCAAGAGGACAGTCAATGGGAAGTAAGAAGATTTAAAAGACAAGGGGCAAAGAAAAATGCAGTGGTGTGTTTCCATTG
TAGAAAACCTGGTCATGGAATTGCGGATTGCCCTGCTGCCCTTGAAAATCAAGATATGGGCACTAGAATATGTTACAAGT
GTGGGTCCACAGAGCACGAAATAACCAAGTGTAAGGCTAAAGTAGACCCGCCTCTTGGCGAATTTCCTTTTGCAAAATGT
TTTGTTTGTGGAGAAATGGGGCACCTGTCTAGATCTTGTCCTGATAATCCCAAAGGACTCTATGCTGATGGGGTGGTTGC
CAACTTTGTGGCTCTGTGGAACATTTAAAGAAAGATTGCCCTGAAAGTGAGAATTCAGATCGAATGGTCACAGTTGGTCT
GTGGGCAAAGGGAATGAGTGCAGACTATGAAGAAATTTTGGATGCACCAAAACCACAAAAACCCAAAACAAAAATATCTA
AAGATGTTAATTTT

Alignment

ORF - retro_pabe_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.13 %
• Parental protein coverage: 60.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKKDSRREGRRLKRQAAKKNAMVCFHCRKPGHGIADCPAALENQDMGTGICYRCGSTEHEITKCKAKVDP
          L..DS..E.RR.KRQ.AKKNA.VCFHCRKPGHGIADCPAALENQDMGT.ICY.CGSTEHEITKCKAKVDP
Retrocopy LQEDSQWEVRRFKRQGAKKNAVVCFHCRKPGHGIADCPAALENQDMGTRICYKCGSTEHEITKCKAKVDP

Parental  ALGEFPFAKCFVCGEMGHLSRSCPDNPKGLYADG-GGCKLCGSVEHLKKDCPESQNSERMVTVGRWAKGM
          .LGEFPFAKCFVCGEMGHLSRSCPDNPKGLYADG.GGC.LCGSVEHLKKDCPES.NS.RMVTVG.WAKGM
Retrocopy PLGEFPFAKCFVCGEMGHLSRSCPDNPKGLYADG<GGCQLCGSVEHLKKDCPESENSDRMVTVGLWAKGM

Parental  SADYEEILDAPKPQKPKTKIPKVVNF
          SADYEEILDA...........K.VNF
Retrocopy SADYEEILDAXXXXXXXXXXSKDVNF

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	10.84 RPM
SRP007412_cerebellum	0.00 RPM	19.21 RPM
SRP007412_heart	0.00 RPM	9.18 RPM
SRP007412_kidney	0.03 RPM	19.46 RPM
SRP007412_liver	0.03 RPM	27.27 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1476 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1476 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1799
Pan troglodytes	retro_ptro_1205

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476 ,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,