RetrogeneDB ID: retro_ptro_2146

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:45914845..45915332(+)
• Located in intron of: ENSPTRG00000016947

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL1
• Ensembl ID: ENSPTRG00000003895
• Aliases: None
• Description: cofilin 1 (non-muscle) [Source:HGNC Symbol;Acc:1874]

Sequence

>retro_ptro_2146
GTGTCTGTCTCTGATGGTGTCATCAAGGTGTTCAACGACATGAAGGTGTGTAAGTCTTCAACACCAGAGAAGTTGAAGAA
GCGCAAGAAGGCGGTGCTCTTCCGCCTGAGTGAAGACAAGAAGAACATCATCCTGAAGGGGAGGGCAAGGAGATACTGGT
GGGCAATGTGGACCAGACCATCGACGACCCCTATGCCACCTTTGTCAAGATGCTACCGGATAAGGATTGCCTCTACGCCC
TCTATGACGCAACCTATGAGACCAAGAGAGCAAGAAGGAGGACCTGGTGTTTATCTTCTGGGCCACTGAGTCTGTGCCCC
TTAAGAGCAAAATGATCAATGCCAGCTCCAAGGACGCCATCAACAAGAAGCTGACAGGAATCAAGCAAGAATTACAAGCA
AACTACTATGAAGAGGTCAAGGACCACTGCACCCTGGCAGAGAAGCTGGGGGGCAGTGCCATCATCTCCCTGGAGGGCAA
GCCTTTG

Alignment

ORF - retro_ptro_2146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.18 %
• Parental protein coverage: 97.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAVSDGVIKVFNDMKVRKSSTPEEVK-KRKKAVLFCLSEDKKNIILE-EGKEILVGDVGQTVDDPYATFV
          V.VSDGVIKVFNDMKV.KSSTPE..K...K..........K..I....EGKEILVG.V.QT.DDPYATFV
Retrocopy VSVSDGVIKVFNDMKVCKSSTPEKLKKRKKAVLFRLSEDKKNIILKG<EGKEILVGNVDQTIDDPYATFV

Parental  KMLPDKDCRYALYDATYETK-ESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKLTGIKHELQANCYE
          KMLPDKDC.YALYDATYETK.ESKKEDLVFIFWA.ES.PLKSKMI.ASSKDAI.KKLTGIK.ELQAN.YE
Retrocopy KMLPDKDCLYALYDATYETK<ESKKEDLVFIFWATESVPLKSKMINASSKDAINKKLTGIKQELQANYYE

Parental  EVKDRCTLAEKLGGSAVISLEGKPL
          EVKD.CTLAEKLGGSA.ISLEGKPL
Retrocopy EVKDHCTLAEKLGGSAIISLEGKPL

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	0.20 RPM	403.03 RPM
SRP007412_cerebellum	0.32 RPM	306.79 RPM
SRP007412_heart	0.12 RPM	68.29 RPM
SRP007412_kidney	0.34 RPM	304.15 RPM
SRP007412_liver	0.43 RPM	324.66 RPM
SRP007412_testis	0.42 RPM	79.88 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2146 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2146 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3333

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017334	2 retrocopies	retro_amel_583, retro_amel_816,
Canis familiaris	ENSCAFG00000024955	6 retrocopies	retro_cfam_1544, retro_cfam_366, retro_cfam_660, retro_cfam_67, retro_cfam_943, retro_cfam_964,
Callithrix jacchus	ENSCJAG00000001916	1 retrocopy	retro_cjac_347,
Equus caballus	ENSECAG00000019900	1 retrocopy	retro_ecab_442,
Felis catus	ENSFCAG00000013272	3 retrocopies	retro_fcat_1456, retro_fcat_303, retro_fcat_991,
Homo sapiens	ENSG00000172757	6 retrocopies	retro_hsap_2617, retro_hsap_287, retro_hsap_3333, retro_hsap_336, retro_hsap_384, retro_hsap_400,
Gorilla gorilla	ENSGGOG00000023183	5 retrocopies	retro_ggor_1832, retro_ggor_326, retro_ggor_357, retro_ggor_389, retro_ggor_397,
Myotis lucifugus	ENSMLUG00000024685	6 retrocopies	retro_mluc_1905, retro_mluc_2114, retro_mluc_216, retro_mluc_2218, retro_mluc_455, retro_mluc_507,
Macaca mulatta	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mustela putorius furo	ENSMPUG00000011502	2 retrocopies	retro_mputfur_1485, retro_mputfur_575,
Nomascus leucogenys	ENSNLEG00000005852	5 retrocopies	retro_nleu_139, retro_nleu_1494, retro_nleu_1571, retro_nleu_1777, retro_nleu_636,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Otolemur garnettii	ENSOGAG00000016503	8 retrocopies	retro_ogar_1442, retro_ogar_1581, retro_ogar_1648, retro_ogar_2192, retro_ogar_302, retro_ogar_405, retro_ogar_453, retro_ogar_828,
Pongo abelii	ENSPPYG00000003047	5 retrocopies	retro_pabe_1732, retro_pabe_2747, retro_pabe_316, retro_pabe_325, retro_pabe_386,
Pan troglodytes	ENSPTRG00000003895	5 retrocopies	retro_ptro_1764, retro_ptro_2146 , retro_ptro_236, retro_ptro_298, retro_ptro_306,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Ictidomys tridecemlineatus	ENSSTOG00000027968	4 retrocopies	retro_itri_144, retro_itri_1456, retro_itri_1734, retro_itri_685,
Tursiops truncatus	ENSTTRG00000016931	2 retrocopies	retro_ttru_1256, retro_ttru_598,