RetrogeneDB ID: retro_pabe_3341

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:68957468..68958075(-)
• Located in intron of: ENSPPYG00000018644

Retrocopy information

• Ensembl ID: ENSPPYG00000018643
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTTG1
• Ensembl ID: ENSPPYG00000016009
• Aliases: None
• Description: pituitary tumor-transforming 1 [Source:HGNC Symbol;Acc:9690]

Sequence

>retro_pabe_3341
ATGGCTACTCTGATCTATGTTGATAAGGAAAATGAAGAACCAGGCACCCTTGTGGCTACAAAGGATGGGCTGAAGCTGGG
GTCTGGACCTTCAATCAAAGCCTTAGATGGGAGATCTCAAGTTTCAACATCACGTTTTGGCAAAACATTCGATGCTGCAA
CAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTCAGTAAAGACCAATGGACCC
CTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAAGCAAAAAGCTCTGTTCCTGCCTC
AGACGATGCCTATCCAGAAATAGAAAAATTATTTCCCTTCAATCCTCTAGGCTTTGAGAGTTTTAACCTGCCTGAGGAGC
ACCAGATTGCACATCTTCCCTTGAGTGGAGTGCCTCTGATGATCCTTGACGAGGAGAGAGAGCTTGAAAAGCTGTTTCAG
CTAGGCCCCCCCTTTACCTTTGAAAATGCCCTCTCCACCATGGGAATCCAATCTGTTGCAGTCTCCTTCAAGCATTCTGT
TGACCCTGGATGTTGAATTGCCACCTGTTTGCTCTGACATAGATATT

Alignment

ORF - retro_pabe_3341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATLIYVDKENGEPGTRVAAKDGLKLGSGPSIKALDGRSQVSTPCFGKTFDAPPALPKATRKALGTVNRA
          MATLIYVDKEN.EPGT.VA.KDGLKLGSGPSIKALDGRSQVST..FGKTFDA..ALPKATRKALGTVNRA
Retrocopy MATLIYVDKENEEPGTLVATKDGLKLGSGPSIKALDGRSQVSTSRFGKTFDAATALPKATRKALGTVNRA

Parental  TEKSVKTKGPIKQKQPSFSAKKMTEKTVKAKSSVPASDDAYPEIEKFFPFNPLDFESFDLPEEHQIAHLP
          TEKSVKT.GP.KQKQPSFSAKKMTEKTVKAKSSVPASDDAYPEIEK.FPFNPL.FESF.LPEEHQIAHLP
Retrocopy TEKSVKTNGPLKQKQPSFSAKKMTEKTVKAKSSVPASDDAYPEIEKLFPFNPLGFESFNLPEEHQIAHLP

Parental  LSGVPLMILDEERELEKLFQLG-PPSPVKMPSPPWESNPLQSPSSILSTLDVELPPVCCDIDI
          LSGVPLMILDEERELEKLFQLG.PP.P.KMPSPPWESN.LQSPSSIL.TLDVELPPVC.DIDI
Retrocopy LSGVPLMILDEERELEKLFQLG>PPLPLKMPSPPWESNLLQSPSSILLTLDVELPPVCSDIDI

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	0.11 RPM	1.16 RPM
SRP007412_cerebellum	0.24 RPM	2.07 RPM
SRP007412_heart	0.00 RPM	0.36 RPM
SRP007412_kidney	0.03 RPM	0.43 RPM
SRP007412_liver	0.03 RPM	0.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3341 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3341 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4068
Pan troglodytes	retro_ptro_2757
Gorilla gorilla	retro_ggor_2731
Macaca mulatta	retro_mmul_2347

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012184	2 retrocopies	retro_btau_122, retro_btau_53,
Canis familiaris	ENSCAFG00000017264	1 retrocopy	retro_cfam_1586,
Choloepus hoffmanni	ENSCHOG00000009464	11 retrocopies	retro_chof_1246, retro_chof_1518, retro_chof_1679, retro_chof_2027, retro_chof_2161, retro_chof_2304, retro_chof_2459, retro_chof_2463, retro_chof_2690, retro_chof_426, retro_chof_526,
Callithrix jacchus	ENSCJAG00000019165	4 retrocopies	retro_cjac_2184, retro_cjac_2293, retro_cjac_2530, retro_cjac_3062,
Cavia porcellus	ENSCPOG00000011971	2 retrocopies	retro_cpor_1151, retro_cpor_820,
Dasypus novemcinctus	ENSDNOG00000024080	4 retrocopies	retro_dnov_1400, retro_dnov_2553, retro_dnov_918, retro_dnov_949,
Dipodomys ordii	ENSDORG00000007968	1 retrocopy	retro_dord_779,
Felis catus	ENSFCAG00000024074	3 retrocopies	retro_fcat_1153, retro_fcat_846, retro_fcat_878,
Homo sapiens	ENSG00000164611	4 retrocopies	retro_hsap_3823, retro_hsap_4068, retro_hsap_67, retro_hsap_881,
Gorilla gorilla	ENSGGOG00000016937	5 retrocopies	retro_ggor_2022, retro_ggor_2572, retro_ggor_2573, retro_ggor_2731, retro_ggor_714,
Loxodonta africana	ENSLAFG00000011135	1 retrocopy	retro_lafr_258,
Macropus eugenii	ENSMEUG00000005993	1 retrocopy	retro_meug_577,
Microcebus murinus	ENSMICG00000006363	1 retrocopy	retro_mmur_181,
Myotis lucifugus	ENSMLUG00000002317	1 retrocopy	retro_mluc_1080,
Macaca mulatta	ENSMMUG00000023077	3 retrocopies	retro_mmul_1052, retro_mmul_1629, retro_mmul_2347,
Mustela putorius furo	ENSMPUG00000013241	3 retrocopies	retro_mputfur_1358, retro_mputfur_429, retro_mputfur_813,
Nomascus leucogenys	ENSNLEG00000004396	5 retrocopies	retro_nleu_218, retro_nleu_2487, retro_nleu_2527, retro_nleu_2528, retro_nleu_830,
Oryctolagus cuniculus	ENSOCUG00000014877	2 retrocopies	retro_ocun_150, retro_ocun_1565,
Otolemur garnettii	ENSOGAG00000012307	2 retrocopies	retro_ogar_2802, retro_ogar_990,
Pongo abelii	ENSPPYG00000016009	4 retrocopies	retro_pabe_2428, retro_pabe_3071, retro_pabe_3341 , retro_pabe_674,
Pan troglodytes	ENSPTRG00000017492	4 retrocopies	retro_ptro_1974, retro_ptro_2601, retro_ptro_2757, retro_ptro_610,
Pteropus vampyrus	ENSPVAG00000015938	2 retrocopies	retro_pvam_431, retro_pvam_704,
Sarcophilus harrisii	ENSSHAG00000010267	1 retrocopy	retro_shar_104,
Tupaia belangeri	ENSTBEG00000015966	2 retrocopies	retro_tbel_2399, retro_tbel_771,
Tursiops truncatus	ENSTTRG00000011570	1 retrocopy	retro_ttru_259,
Vicugna pacos	ENSVPAG00000009594	2 retrocopies	retro_vpac_178, retro_vpac_33,