RetrogeneDB ID: retro_pabe_1241

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:41400781..41401446(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AZI2
• Ensembl ID: ENSPPYG00000014053
• Aliases: None
• Description: 5-azacytidine-induced protein 2 [Source:RefSeq peptide;Acc:NP_001127269]

Sequence

>retro_pabe_1241
AGCTGTAACCTGAAGATCCAAGGTTTGGAACAAGAGTTGATGATGAAAGAATGTAACGATCTCAAAATAGAACTACGCAA
AAACCAAACAAACCTATCTGTATCAAGAAGACAATCTTGAAGAGCAGAGATCTCTGAAGAGTAAGAACTTCAAGTGATAA
TACGCAGAATGTATACTGGCAACTGAAGAGATAAATGTCTAATTTATATCTGGTGACTCAAGTGCTAGCTGAACTATTAA
GAAAACTGAAAACCCCAACTGCAATCAAGAAAGCCTGCACCTCAGTAGGATACATTGAAGACCCTTGGAAAGACGGCACA
AAACTGCACATGATGAATTTTACTGCAACATACACAAGACATCTCCTTCTCTCACCAAATGGCAAAACTCTTTGTTATAC
TACATCTTCCCCTTTACCAGGAGATATAAAGGTTTTATCAGAGAAAGCAGTCCTCCAATCATGGACAGATAATGAGAGAG
CCATTCCTAATGAGGGCACACACTCTTATGGCAGAAACTCTCTGGAAGATCATTTTGAGTATTCCCAATCCCTCCTGACT
CAAGTGAGACAGCATTTAGGGAAATTAACAGTAAAATTTTGCCTTTTAACCAATGTACCACTACTGCATTACTTGGATCA
ACATAATCAAAATTTCCTTTTTAAG

Alignment

ORF - retro_pabe_1241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 58.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SCDLKIHGLEQELELMRKECSDLKIELQK-AKQTDPYQEDNL-KSRDLQKLSISSDNMQHAYWELKREMS
          SC.LKI.GLEQEL..M.KEC.DLKIEL.K..KQT..YQEDNL.KSRDL.....SSDN.Q..YW.LKR.MS
Retrocopy SCNLKIQGLEQEL--MMKECNDLKIELRK>TKQTYLYQEDNL>KSRDL*RVRTSSDNTQNVYWQLKR*MS

Parental  NLHLVTQVQAELLRKLKTSTAIKKACAPVGCSEDLGRDSTKLHLMNFTATYTRHPPVSPNGKALCHTASS
          NL.LVTQV.AELLRKLKT.TAIKKAC..VG..ED...D.TKLH.MNFTATYTRH...SPNGK.LC.T.SS
Retrocopy NLYLVTQVLAELLRKLKTPTAIKKACTSVGYIEDPWKDGTKLHMMNFTATYTRHLLLSPNGKTLCYTTSS

Parental  PLPGDVKVLSEKAILQSWTDNERSIPNDGTCFQEHSSYGRNSLEDNSW-VFPSPPKSSETAFGETKTKTL
          PLPGD.KVLSEKA.LQSWTDNER.IPN.GT....HS.YGRNSLED....VFP.PP.SSETAF.E...K.L
Retrocopy PLPGDIKVLSEKAVLQSWTDNERAIPNEGT----HS-YGRNSLEDHFE<VFPIPPDSSETAFREINSKIL

Parental  P-LPNLPPLHYLDQHNQNCLYK
          P.L.N.P.LHYLDQHNQN.L.K
Retrocopy P>LTNVPLLHYLDQHNQNFLFK

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	7.24 RPM
SRP007412_cerebellum	0.00 RPM	16.78 RPM
SRP007412_heart	0.00 RPM	3.70 RPM
SRP007412_kidney	0.00 RPM	5.70 RPM
SRP007412_liver	0.00 RPM	3.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1241 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1241 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010432	2 retrocopies	retro_chof_1794, retro_chof_234,
Dasypus novemcinctus	ENSDNOG00000011053	2 retrocopies	retro_dnov_1377, retro_dnov_542,
Homo sapiens	ENSG00000163512	2 retrocopies	retro_hsap_1491, retro_hsap_1564,
Gorilla gorilla	ENSGGOG00000022881	2 retrocopies	retro_ggor_1145, retro_ggor_1189,
Loxodonta africana	ENSLAFG00000008538	2 retrocopies	retro_lafr_529, retro_lafr_925,
Myotis lucifugus	ENSMLUG00000000043	3 retrocopies	retro_mluc_1707, retro_mluc_435, retro_mluc_611,
Macaca mulatta	ENSMMUG00000000056	1 retrocopy	retro_mmul_2135,
Monodelphis domestica	ENSMODG00000015075	1 retrocopy	retro_mdom_1786,
Nomascus leucogenys	ENSNLEG00000004069	1 retrocopy	retro_nleu_1714,
Oryctolagus cuniculus	ENSOCUG00000014956	1 retrocopy	retro_ocun_1778,
Otolemur garnettii	ENSOGAG00000005896	1 retrocopy	retro_ogar_3078,
Pongo abelii	ENSPPYG00000014053	2 retrocopies	retro_pabe_1241 , retro_pabe_3784,
Pan troglodytes	ENSPTRG00000014707	1 retrocopy	retro_ptro_1052,
Tursiops truncatus	ENSTTRG00000016434	1 retrocopy	retro_ttru_1093,