RetrogeneDB ID: retro_pabe_3

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:117319178..117319451(-)
• Located in intron of: ENSPPYG00000015703

Retrocopy information

• Ensembl ID: ENSPPYG00000015704
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HMGN2
• Ensembl ID: ENSPPYG00000001682
• Aliases: None
• Description: non-histone chromosomal protein HMG-17 [Source:RefSeq peptide;Acc:NP_001125775]

Sequence

>retro_pabe_3
ATGCCCAAGAGAAAGGCTGAAGGGGATGCTAAAGGAGATAAAGCCAAGGTCAAGGACGAACCACAAAGAAGATCTGCGAG
GTTGTCTGCTAAACCTGCTCCTCCAAAGCCAAAGCCCAGGCCTAAAAAGGCCCCTGCAAAGAAGGGAGAGAAGGTACCCA
AAGGGAAAAAGGGAAAAGCTGATGCTGGCAAGGAGGGGAATAACCCTGCAGAAAATGGAGATGTCAAAACAGATCAGGCA
CAGAAAGCTGAAGGTGCTGGAGATGCCAAGTGA

Alignment

ORF - retro_pabe_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGKKGKADAGKEGNNPA
          MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKP.P.PKKAPAKKGEKVPKGKKGKADAGKEGNNPA
Retrocopy MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPKPRPKKAPAKKGEKVPKGKKGKADAGKEGNNPA

Parental  ENGDAKTDQAQKAEGAGDAK
          ENGD.KTDQAQKAEGAGDAK
Retrocopy ENGDVKTDQAQKAEGAGDAK

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	13.49 RPM
SRP007412_cerebellum	0.00 RPM	12.52 RPM
SRP007412_heart	0.09 RPM	12.19 RPM
SRP007412_kidney	0.00 RPM	20.78 RPM
SRP007412_liver	0.00 RPM	23.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3372
Pan troglodytes	retro_ptro_2292

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001787	3 retrocopies	retro_dord_10, retro_dord_401, retro_dord_511,
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Gorilla gorilla	ENSGGOG00000000971	11 retrocopies	retro_ggor_114, retro_ggor_146, retro_ggor_162, retro_ggor_166, retro_ggor_182, retro_ggor_186, retro_ggor_197, retro_ggor_23, retro_ggor_38, retro_ggor_40, retro_ggor_54,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Otolemur garnettii	ENSOGAG00000032571	14 retrocopies	retro_ogar_1438, retro_ogar_1445, retro_ogar_1603, retro_ogar_1668, retro_ogar_1687, retro_ogar_1998, retro_ogar_2097, retro_ogar_2210, retro_ogar_2231, retro_ogar_2424, retro_ogar_287, retro_ogar_2989, retro_ogar_3411, retro_ogar_52,
Pongo abelii	ENSPPYG00000001682	16 retrocopies	retro_pabe_1182, retro_pabe_1511, retro_pabe_1977, retro_pabe_1989, retro_pabe_206, retro_pabe_2263, retro_pabe_23, retro_pabe_2601, retro_pabe_3 , retro_pabe_3480, retro_pabe_366, retro_pabe_396, retro_pabe_533, retro_pabe_535, retro_pabe_589, retro_pabe_696,
Tarsius syrichta	ENSTSYG00000011519	42 retrocopies	retro_tsyr_114, retro_tsyr_1156, retro_tsyr_1165, retro_tsyr_1199, retro_tsyr_1227, retro_tsyr_1255, retro_tsyr_1270, retro_tsyr_13, retro_tsyr_1357, retro_tsyr_138, retro_tsyr_1382, retro_tsyr_1394, retro_tsyr_143, retro_tsyr_1487, retro_tsyr_1488, retro_tsyr_1506, retro_tsyr_1510, retro_tsyr_1551, retro_tsyr_1618, retro_tsyr_163, retro_tsyr_168, retro_tsyr_1680, retro_tsyr_1878, retro_tsyr_1881, retro_tsyr_1970, retro_tsyr_2019, retro_tsyr_2134, retro_tsyr_256, retro_tsyr_280, retro_tsyr_325, retro_tsyr_333, retro_tsyr_594, retro_tsyr_611, retro_tsyr_668, retro_tsyr_675, retro_tsyr_726, retro_tsyr_772, retro_tsyr_83, retro_tsyr_857, retro_tsyr_927, retro_tsyr_959, retro_tsyr_97,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,