RetrogeneDB ID: retro_pabe_3390

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:25685590..25685875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFA5
• Ensembl ID: ENSPPYG00000017956
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001125332]

Sequence

>retro_pabe_3390
AAGAGGCTAAGAATATTGTACACAAAGATCCTTGATGTTCTTAAGCAAACCCCTTAAAAAGCAGTATATAGAAAGTATAC
TGAACAGACTGCAAATGAGAAGCTGGCTATGGTTAAAGCAGAACCAGATGTTAAAAAATTAGAACACCAACTTCAAGGTG
TTCAAATAAAAGAGGTGATTCTTCAGGTTGAAAGTGAACTAAGTCTGGCAAGAAAAATGATACAGCGGAAATGATAGGAG
ATGTTCATGGAAGAGCCTCCTGCCAATCAATGGAAATGGCCAATG

Alignment

ORF - retro_pabe_3390 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.63 %
• Parental protein coverage: 81.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVKAEPDVKKLEDQLQGGQLEEVILQAEHELNLA
          .RLRILYTKILDVL...P..A.YRKYTEQ..NEKLAMVKAEPDVKKLE.QLQG.Q..EVILQ.E.EL.LA
Retrocopy KRLRILYTKILDVLKQTP*KAVYRKYTEQTANEKLAMVKAEPDVKKLEHQLQGVQIKEVILQVESELSLA

Parental  RKMKEWKLWEPLVEEPPADQWKWPI
          RKM...K..E...EEPPA.QWKWP.
Retrocopy RKMIQRK**EMFMEEPPANQWKWPM

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	36.16 RPM
SRP007412_cerebellum	0.00 RPM	33.56 RPM
SRP007412_heart	0.00 RPM	40.43 RPM
SRP007412_kidney	0.00 RPM	30.40 RPM
SRP007412_liver	0.00 RPM	10.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3390 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3390 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3390 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4248
Pan troglodytes	retro_ptro_2888
Gorilla gorilla	retro_ggor_2848

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004512	2 retrocopies	retro_amel_1543, retro_amel_695,
Bos taurus	ENSBTAG00000009334	5 retrocopies	retro_btau_1258, retro_btau_1613, retro_btau_537, retro_btau_808, retro_btau_950,
Canis familiaris	ENSCAFG00000025112	4 retrocopies	retro_cfam_302, retro_cfam_445, retro_cfam_882, retro_cfam_921,
Callithrix jacchus	ENSCJAG00000017449	1 retrocopy	retro_cjac_65,
Felis catus	ENSFCAG00000027125	5 retrocopies	retro_fcat_1081, retro_fcat_1278, retro_fcat_244, retro_fcat_550, retro_fcat_799,
Homo sapiens	ENSG00000128609	10 retrocopies	retro_hsap_1065, retro_hsap_1687, retro_hsap_2671, retro_hsap_3218, retro_hsap_3627, retro_hsap_3950, retro_hsap_3997, retro_hsap_4248, retro_hsap_745, retro_hsap_746,
Gorilla gorilla	ENSGGOG00000022922	9 retrocopies	retro_ggor_1264, retro_ggor_1864, retro_ggor_2185, retro_ggor_2447, retro_ggor_2654, retro_ggor_2683, retro_ggor_2848, retro_ggor_624, retro_ggor_840,
Loxodonta africana	ENSLAFG00000030971	1 retrocopy	retro_lafr_275,
Monodelphis domestica	ENSMODG00000015384	4 retrocopies	retro_mdom_1292, retro_mdom_1429, retro_mdom_1804, retro_mdom_525,
Mustela putorius furo	ENSMPUG00000006811	4 retrocopies	retro_mputfur_1151, retro_mputfur_1353, retro_mputfur_683, retro_mputfur_939,
Mus musculus	ENSMUSG00000023089	2 retrocopies	retro_mmus_2951, retro_mmus_853,
Otolemur garnettii	ENSOGAG00000033137	6 retrocopies	retro_ogar_1346, retro_ogar_1504, retro_ogar_1791, retro_ogar_2047, retro_ogar_2676, retro_ogar_649,
Pongo abelii	ENSPPYG00000017956	10 retrocopies	retro_pabe_1389, retro_pabe_2216, retro_pabe_2666, retro_pabe_2794, retro_pabe_2795, retro_pabe_2975, retro_pabe_3283, retro_pabe_3390 , retro_pabe_3728, retro_pabe_887,
Pan troglodytes	ENSPTRG00000019637	10 retrocopies	retro_ptro_1141, retro_ptro_1800, retro_ptro_2235, retro_ptro_2452, retro_ptro_2682, retro_ptro_2714, retro_ptro_2888, retro_ptro_2937, retro_ptro_529, retro_ptro_725,
Rattus norvegicus	ENSRNOG00000005698	3 retrocopies	retro_rnor_1041, retro_rnor_2154, retro_rnor_2290,
Sus scrofa	ENSSSCG00000016607	2 retrocopies	retro_sscr_1029, retro_sscr_693,
Ictidomys tridecemlineatus	ENSSTOG00000027404	1 retrocopy	retro_itri_911,