RetrogeneDB ID: retro_pabe_2258

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:134783008..134783433(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIP7
• Ensembl ID: ENSPPYG00000007503
• Aliases: None
• Description: 60S ribosome subunit biogenesis protein NIP7 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R9J1]

Sequence

>retro_pabe_2258
CTGCACAACGACCGGGTGTACTATGTGAGTGAGAAGCTTGTGAAGCTGGACGCCAATATCTCCGGGGACAAGCTGGTGTC
ACTGGGAACCTGCTTTGGAAAAGTCGCTAAGACCCACAAGTTTCGGTTCACGTCACAGCCCTGAATTACCTTGCACCTTA
TGCCAAGTATAAAGTGTGGATAAAGCGTGGTGCAGAGCAGTCCTTCCTCTATGGGAACCATGTGTTGAAATATGGTCTGG
GTCGAATCACCGAAAATAGTTCTCAGTACCAGGGAGTGGTAGTGTATGCCATGGCAGACATCCCTTTGGGTTTTGGGGTG
GCAGCAAAATCTACACAAGACTGCAGAAAAGTAGACCCCATGGCGATTGTGGTACTTCATCAAGCAGACATTGGGGAATA
TGCACAGCATGAAGAGACGTTGACT

Alignment

ORF - retro_pabe_2258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.51 %
• Parental protein coverage: 78.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHNDRVYYVSEKIMKLAANISGDKLVSLGTCFGKFTKTHKFR-LHVTALDYLAPYAKYKVWIKPGAEQSF
          LHNDRVYYVSEK..KL.ANISGDKLVSLGTCFGK..KTHKFR..HVTAL.YLAPYAKYKVWIK.GAEQSF
Retrocopy LHNDRVYYVSEKLVKLDANISGDKLVSLGTCFGKVAKTHKFR<VHVTALNYLAPYAKYKVWIKRGAEQSF

Parental  LYGNHVLKSGLGRITENTSQYQGVVVYSMADIPLGFGVAAKSTQDCRKVDPMAIVVFHQADIGEYVRHEE
          LYGNHVLK.GLGRITEN.SQYQGVVVY.MADIPLGFGVAAKSTQDCRKVDPMAIVV.HQADIGEY..HEE
Retrocopy LYGNHVLKYGLGRITENSSQYQGVVVYAMADIPLGFGVAAKSTQDCRKVDPMAIVVLHQADIGEYAQHEE

Parental  TLT
          TLT
Retrocopy TLT

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	10.95 RPM
SRP007412_cerebellum	0.00 RPM	6.93 RPM
SRP007412_heart	0.00 RPM	4.52 RPM
SRP007412_kidney	0.00 RPM	11.37 RPM
SRP007412_liver	0.00 RPM	10.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2258 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2258 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2707
Pan troglodytes	retro_ptro_1828
Gorilla gorilla	retro_ggor_1886

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007542	1 retrocopy	retro_amel_938,
Bos taurus	ENSBTAG00000001666	1 retrocopy	retro_btau_353,
Canis familiaris	ENSCAFG00000029835	2 retrocopies	retro_cfam_1346, retro_cfam_1682,
Callithrix jacchus	ENSCJAG00000015364	2 retrocopies	retro_cjac_2466, retro_cjac_4212,
Dasypus novemcinctus	ENSDNOG00000006821	2 retrocopies	retro_dnov_2114, retro_dnov_74,
Homo sapiens	ENSG00000132603	2 retrocopies	retro_hsap_2707, retro_hsap_3648,
Gorilla gorilla	ENSGGOG00000022785	2 retrocopies	retro_ggor_1886, retro_ggor_2464,
Microcebus murinus	ENSMICG00000009664	1 retrocopy	retro_mmur_5,
Myotis lucifugus	ENSMLUG00000011835	3 retrocopies	retro_mluc_1119, retro_mluc_2171, retro_mluc_2508,
Macaca mulatta	ENSMMUG00000016635	2 retrocopies	retro_mmul_1801, retro_mmul_192,
Monodelphis domestica	ENSMODG00000002782	2 retrocopies	retro_mdom_1011, retro_mdom_1709,
Mus musculus	ENSMUSG00000031917	2 retrocopies	retro_mmus_1858, retro_mmus_2281,
Nomascus leucogenys	ENSNLEG00000005492	2 retrocopies	retro_nleu_1579, retro_nleu_510,
Oryctolagus cuniculus	ENSOCUG00000017652	5 retrocopies	retro_ocun_1013, retro_ocun_1262, retro_ocun_1292, retro_ocun_491, retro_ocun_721,
Otolemur garnettii	ENSOGAG00000008066	2 retrocopies	retro_ogar_1619, retro_ogar_2453,
Pongo abelii	ENSPPYG00000007503	2 retrocopies	retro_pabe_2258 , retro_pabe_2995,
Pan troglodytes	ENSPTRG00000008279	2 retrocopies	retro_ptro_1828, retro_ptro_2473,
Rattus norvegicus	ENSRNOG00000020391	8 retrocopies	retro_rnor_1279, retro_rnor_1566, retro_rnor_1567, retro_rnor_1674, retro_rnor_1676, retro_rnor_485, retro_rnor_655, retro_rnor_865,
Sorex araneus	ENSSARG00000000303	1 retrocopy	retro_sara_665,
Ictidomys tridecemlineatus	ENSSTOG00000012871	1 retrocopy	retro_itri_1368,
Tursiops truncatus	ENSTTRG00000010012	2 retrocopies	retro_ttru_1783, retro_ttru_676,