RetrogeneDB ID: retro_ptro_1040

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:26584915..26585184(-)
• Located in intron of: ENSPTRG00000006846

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN2
• Ensembl ID: ENSPTRG00000000386
• Aliases: None
• Description: high mobility group nucleosomal binding domain 2 [Source:HGNC Symbol;Acc:4986]

Sequence

>retro_ptro_1040
ATGCCCAAGAGAAAGGCTGAAGGGGATGCTAAGGGAGATAAAGCCAAGGTGAAGGACGAACCACAGAGAAGATCCGCGAG
GTTGTCTGCTAAACCTGCTCCTCCAAAGCCAGAGCCCAAGCCTAAAAAGGCCCCTGCAAAGAAGGGAGAGAAGGTACCAA
AGGGAAAAAGGGAAAAGCTGATGCTGGCAAGGAGGGGAATAACCCTGCAGAAAATGGAGATGCCAAAACAGACCAGGCAC
AGAAAGCTGAAGGTGCTGGAGATGCCAAG

Alignment

ORF - retro_ptro_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGK-KGKADAGKEGNNP
          MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGK.KGKADAGKEGNNP
Retrocopy MPKRKAEGDAKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGK<KGKADAGKEGNNP

Parental  AENGDAKTDQAQKAEGAGDAK
          AENGDAKTDQAQKAEGAGDAK
Retrocopy AENGDAKTDQAQKAEGAGDAK

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	0.71 RPM	61.63 RPM
SRP007412_cerebellum	0.22 RPM	44.95 RPM
SRP007412_heart	0.44 RPM	43.75 RPM
SRP007412_kidney	1.07 RPM	98.88 RPM
SRP007412_liver	0.20 RPM	50.51 RPM
SRP007412_testis	0.32 RPM	70.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1040 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1040 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 151 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,
Homo sapiens	ENSG00000198830	51 retrocopies	retro_hsap_100, retro_hsap_114, retro_hsap_1208, retro_hsap_1368, retro_hsap_1395, retro_hsap_1427, retro_hsap_1471, retro_hsap_1492, retro_hsap_1512, retro_hsap_1517, retro_hsap_1518, retro_hsap_1586, retro_hsap_1670, retro_hsap_1684, retro_hsap_1787, retro_hsap_1834, retro_hsap_1931, retro_hsap_1934, retro_hsap_2082, retro_hsap_2116, retro_hsap_2296, retro_hsap_2309, retro_hsap_233, retro_hsap_2564, retro_hsap_2592, retro_hsap_2728, retro_hsap_273, retro_hsap_2755, retro_hsap_2779, retro_hsap_2849, retro_hsap_2914, retro_hsap_318, retro_hsap_3189, retro_hsap_3339, retro_hsap_3372, retro_hsap_3412, retro_hsap_3515, retro_hsap_3616, retro_hsap_3755, retro_hsap_3896, retro_hsap_4124, retro_hsap_4138, retro_hsap_4297, retro_hsap_4791, retro_hsap_4914, retro_hsap_601, retro_hsap_688, retro_hsap_689, retro_hsap_718, retro_hsap_793, retro_hsap_849,
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,
Pan troglodytes	ENSPTRG00000000386	54 retrocopies	retro_ptro_1011, retro_ptro_1024, retro_ptro_1026, retro_ptro_1027, retro_ptro_1040 , retro_ptro_1053, retro_ptro_1067, retro_ptro_1094, retro_ptro_1197, retro_ptro_1235, retro_ptro_128, retro_ptro_1291, retro_ptro_1292, retro_ptro_1495, retro_ptro_1516, retro_ptro_1532, retro_ptro_1549, retro_ptro_1625, retro_ptro_1633, retro_ptro_1837, retro_ptro_1844, retro_ptro_1863, retro_ptro_1880, retro_ptro_1929, retro_ptro_1970, retro_ptro_203, retro_ptro_2255, retro_ptro_229, retro_ptro_2292, retro_ptro_2317, retro_ptro_2387, retro_ptro_2445, retro_ptro_2461, retro_ptro_2549, retro_ptro_257, retro_ptro_2650, retro_ptro_2801, retro_ptro_2812, retro_ptro_2840, retro_ptro_2913, retro_ptro_2970, retro_ptro_3187, retro_ptro_3276, retro_ptro_445, retro_ptro_493, retro_ptro_495, retro_ptro_512, retro_ptro_543, retro_ptro_552, retro_ptro_59, retro_ptro_590, retro_ptro_827, retro_ptro_939, retro_ptro_958,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,