RetrogeneDB ID: retro_pabe_1442

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:24737478..24737993(+)
• Located in intron of: ENSPPYG00000008129

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME4
• Ensembl ID: ENSPPYG00000006908
• Aliases: None
• Description: NME/NM23 nucleoside diphosphate kinase 4 [Source:HGNC Symbol;Acc:7852]

Sequence

>retro_pabe_1442
CTCTTCGGGCACGCCACCGCTGCCGGGCCTGCTGTACGACCCGCGGGCTCTGGGCCATGCCTGCTCTTGCGCCCGGCTCA
GGAGGACCCTTGTTGATCCAGGAGTGGACCCTGGTCTCATTGAAGCCAGTTGGGGTCTTGTGGCGGCCTGTTAGGGATGT
GATCCAGCGCTTTGGAGGCAGGGCTTCAAGCTGGTAGAGATGAAGATCCTGTGGCCGGCCAGAAAGCGTCCTTGCTGAAC
ACTACCAGGACCTGTGAAGGAAGCCCTTCTACCCAGCCCTCCTTAGCTATGTGAGCTCCAGGCCTGTTGATGGCCATGGT
CTGGGAAGGGTACAATGTGATCCACGCCTCGAGGGCCATGATAGGATACACTGACAGGGCTGAGGCTGACTCTGTGACCA
TATGGGGAGACTTCAGCGACGTCCACATCAGCAGGAACATCATTCACACCAGCTATTCAGGGTAGGGGATCAGAAAGAGA
TCCAGCTGTGGTTTGAAAGCAGTGAGCTGGTGAAC

Alignment

ORF - retro_pabe_1442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.32 %
• Parental protein coverage: 91.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LFWRSALQGLRCGPRAQGPSLLARHS-SGGPSWTRERTLVAVKPDGVQRRLVGDVIQRFE-RRGFTLVGM
          LF......G....P...GP.LL.R...SGGP....E.TLV..KP.GV..R.V.DVIQRF..R.GF.LV.M
Retrocopy LFGHATAAGPAVRPAGSGPCLLLRPA<SGGPLLIQEWTLVSLKPVGVLWRPVRDVIQRFG<RQGFKLVEM

Parental  KML-QAPETEIALHYQDLRRKTFYPDLVRYMSSGPG-VAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRG
          K.L...PE...A.HYQDL.RK.FYP.L..Y.SS.P...AMVWEGYNV..ASRAMIG.TD.AEA...TI.G
Retrocopy KIL>GRPESVLAEHYQDL*RKPFYPALLSYVSSRPV>MAMVWEGYNVIHASRAMIGYTDRAEADSVTIWG

Parental  DFS-VHISRNVIHASDS-VEGAQREIQLWFQSSELVS
          DFS.VHISRN.IH.S.S...G.Q.EIQLWF.SSELV.
Retrocopy DFSDVHISRNIIHTSYS<RVGDQKEIQLWFESSELVN

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	6.75 RPM
SRP007412_cerebellum	0.12 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	9.39 RPM
SRP007412_kidney	0.00 RPM	19.32 RPM
SRP007412_liver	0.03 RPM	10.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1442 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1442 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442 ,
Pongo abelii	ENSPPYG00000006961	1 retrocopy	retro_pabe_102,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,