RetrogeneDB ID: retro_pabe_3784

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:83090378..83091250(-)
• 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_3784
AAGAACTCTTTGTTAAAGAAGGGAATAAGATTTTTGGAAGAAAAGCTAATAGCTCGATTTGATGAAGAAACAAGTTTCGT
GGGATGAGAACAAGTAAATAAGGCCTATCGTGCATATCGAGAGGTTTGCATTGATAGAGATAATTTGAAGAGCAAACTGG
ACAAAATAGATAAAGACAACTCTGAATCTTTGAAAGTATTGAATGAGCAGCTACAATCTAAAGAAGTAGAACTCCTCCAG
CTGAGGACAGAGGTGGAAACTCAGCAGGTGATGAGGAATTTAAATCCACCTTCATCAAACTGGGAGGTGGAAAAGTTGAG
CTGTGACCTGAAGATCCATGGTTTGGAACAAGAGCTGGAACTGATGAGAAAAGAACGTAGCGATCTCAAAATAGAACTAC
AGAAAGCCAAACAAACGATCCATATCAGGAAGACAATCTGAAGAGCAGAGATCTCCAAAAACTAAGCATTTCAAGTGATA
ATATGCAGCATGCATACTGGGAACTGAAGAGAGAAATGTCTAATTTACATCTGGTGACTCAAGTACAAGGTGAACTACTA
AGAAAACTGAAAACCTCAACTGCAATCAAGAAAGCCTGTGCCCCTGTAGGATGCAGTGAAGACCTTGGAAGAGACAGCAC
AAAACTGCACTTGATGAATTTTACTGCAACATACACAAGACATCCCCCTGTCTCACCAAATGGCAAAGCTCTTTGTCATA
CCGCATCATCCCCTTTACCAGGAGATGTAAAGGTTTCATCAGAGAAAGCAATCCTCCAATCATGGACAGACAATGAGAGA
TCCATTCCTAATGATGGTACATGCTTTCACGAACACAGTTCTTATGGCAGAAATTCTCTGGAAGACAATTCC

Alignment

ORF - retro_pabe_3784 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.89 %
• Parental protein coverage: 74.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ENSLLKKRIRFLEEKLIARFDEETSSVGREQVNKAYHAYREVCIDRDNLKSKLDKMNKDNSESLKVLNEQ
          .NSLLKK.IRFLEEKLIARFDEETS.VG.EQVNKAY.AYREVCIDRDNLKSKLDK..KDNSESLKVLNEQ
Retrocopy KNSLLKKGIRFLEEKLIARFDEETSFVG*EQVNKAYRAYREVCIDRDNLKSKLDKIDKDNSESLKVLNEQ

Parental  LQSKEVELLQLRTEVETQQVMRNLNPPSSNWEVEKLSCDLKIHGLEQELELMRKECSDLKIELQKAKQT-
          LQSKEVELLQLRTEVETQQVMRNLNPPSSNWEVEKLSCDLKIHGLEQELELMRKE.SDLKIELQKAKQT.
Retrocopy LQSKEVELLQLRTEVETQQVMRNLNPPSSNWEVEKLSCDLKIHGLEQELELMRKERSDLKIELQKAKQT<

Parental  DPYQEDNLKSRDLQKLSISSDNMQHAYWELKREMSNLHLVTQVQAELLRKLKTSTAIKKACAPVGCSEDL
          DPYQEDNLKSRDLQKLSISSDNMQHAYWELKREMSNLHLVTQVQ.ELLRKLKTSTAIKKACAPVGCSEDL
Retrocopy DPYQEDNLKSRDLQKLSISSDNMQHAYWELKREMSNLHLVTQVQGELLRKLKTSTAIKKACAPVGCSEDL

Parental  GRDSTKLHLMNFTATYTRHPPVSPNGKALCHTASSPLPGDVKVLSEKAILQSWTDNERSIPNDGTCFQEH
          GRDSTKLHLMNFTATYTRHPPVSPNGKALCHTASSPLPGDVKV.SEKAILQSWTDNERSIPNDGTCF.EH
Retrocopy GRDSTKLHLMNFTATYTRHPPVSPNGKALCHTASSPLPGDVKVSSEKAILQSWTDNERSIPNDGTCFHEH

Parental  SSYGRNSLEDNS
          SSYGRNSLEDNS
Retrocopy SSYGRNSLEDNS

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	7.24 RPM
SRP007412_cerebellum	0.00 RPM	16.78 RPM
SRP007412_heart	0.00 RPM	3.70 RPM
SRP007412_kidney	0.03 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_3784 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3784 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3784 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,