RetrogeneDB ID: retro_ptro_2098

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:142438328..142438736(-)
• Located in intron of: ENSPTRG00000016457

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3C
• Ensembl ID: ENSPTRG00000002045
• Aliases: None
• Description: Pan troglodytes histone cluster 1, H3a (HIST1H3A), mRNA. [Source:RefSeq mRNA;Acc:NM_001098568]

Sequence

>retro_ptro_2098
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCGACCGGTGGTAAAGCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCGCTCCGTGAAATTAGAC
GTTATCAGAAGTCCACTGAACTTCTGGTTCGCAAACTTCCCTTCCAGCGTCTGGTGCGAGAAATTGCTCAGGACTTTAAA
ACAGATCTGCGCTTCCAGAGCGCAGCTATCGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTGAGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGACATCCAGCTAGCACGCAGCATACGTGGAG
AACATGCT

Alignment

ORF - retro_ptro_2098 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELL.RKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLVRKLPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNL.AIHAKRVTIMPKDIQLAR.IRGE.A
Retrocopy LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLSAIHAKRVTIMPKDIQLARSIRGEHA

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	0.18 RPM	5.72 RPM
SRP007412_cerebellum	0.07 RPM	0.50 RPM
SRP007412_heart	0.03 RPM	0.61 RPM
SRP007412_kidney	0.16 RPM	1.10 RPM
SRP007412_liver	0.03 RPM	0.69 RPM
SRP007412_testis	0.11 RPM	1.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2098 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2098 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2098 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3102

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014588	7 retrocopies	retro_amel_1023, retro_amel_1026, retro_amel_144, retro_amel_570, retro_amel_687, retro_amel_711, retro_amel_903,
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Monodelphis domestica	ENSMODG00000005983	3 retrocopies	retro_mdom_1037, retro_mdom_1132, retro_mdom_175,
Mustela putorius furo	ENSMPUG00000013811	3 retrocopies	retro_mputfur_1159, retro_mputfur_787, retro_mputfur_881,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pan troglodytes	ENSPTRG00000002045	20 retrocopies	retro_ptro_1045, retro_ptro_1704, retro_ptro_1770, retro_ptro_1867, retro_ptro_1954, retro_ptro_2098 , retro_ptro_2183, retro_ptro_2228, retro_ptro_2229, retro_ptro_2230, retro_ptro_2232, retro_ptro_2233, retro_ptro_2363, retro_ptro_279, retro_ptro_2834, retro_ptro_2936, retro_ptro_2978, retro_ptro_300, retro_ptro_3111, retro_ptro_3164,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640, retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Tursiops truncatus	ENSTTRG00000015889	7 retrocopies	retro_ttru_1094, retro_ttru_1306, retro_ttru_18, retro_ttru_451, retro_ttru_738, retro_ttru_814, retro_ttru_92,