RetrogeneDB ID: retro_pabe_325

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:178620851..178621346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL1
• Ensembl ID: ENSPPYG00000003047
• Aliases: None
• Description: cofilin 1 (non-muscle) [Source:HGNC Symbol;Acc:1874]

Sequence

>retro_pabe_325
GCTTCATGGGTGGCCGTCTCTGATGGCGTCATCAAGGTGTTCAAGGACATGAAGATGCGTAAGTCTTCAACACCAGAGGA
GGCGAAGAAGCGCAAGAAGGTGGTGTTCTTCTGCCTGAGTGAGGACAAGAAGAACATTATCCTGGAGGAGGGCAAGGAGA
TCCTGGTAGGCGATGTGGGCCAGACTGTCGACAACCTCTACGCCACCTTTGTCAAGATGCTGCCATATAAGGACTACCGC
TACGCCCTCTATGACACAACCTACGAGACCAAGGAGAGCAAGGAGGAGGACCTGGTGTTTATCTTCTGGGCCCCTGAGTC
TGCGCCCCTTAAGAGCAAAATAATCTATGCCAGCTCCAAGGACGCCATCAAGAAGAAGCTGACAGGGATCAAGCATGCAT
TACAAGCAAACTGCTACGAGGAGGTCAAGGACCACTGCACCCTGGCAGAGATGCTGGGGGGCAGTGCCGTCATCTCCCTG
GAGGGCAAGCCTTTG

Alignment

ORF - retro_pabe_325 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVGQTVDDPYATF
          AS.VAVSDGVIKVF.DMK.RKSSTPEE.KKRKK.V.FCLSEDKKNIILEEGKEILVGDVGQTVD..YATF
Retrocopy ASWVAVSDGVIKVFKDMKMRKSSTPEEAKKRKKVVFFCLSEDKKNIILEEGKEILVGDVGQTVDNLYATF

Parental  VKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKXTGIKHELQANCYE
          VKMLP.KD.RYALYD.TYETKESK.EDLVFIFWAPESAPLKSK.IYASSKDAIKKK.TGIKH.LQANCYE
Retrocopy VKMLPYKDYRYALYDTTYETKESKEEDLVFIFWAPESAPLKSKIIYASSKDAIKKKLTGIKHALQANCYE

Parental  EVKDRCTLAEKLGGSAVISLEGKPL
          EVKD.CTLAE.LGGSAVISLEGKPL
Retrocopy EVKDHCTLAEMLGGSAVISLEGKPL

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	18.80 RPM	164.77 RPM
SRP007412_cerebellum	6.81 RPM	78.92 RPM
SRP007412_heart	1.87 RPM	28.03 RPM
SRP007412_kidney	9.91 RPM	96.36 RPM
SRP007412_liver	7.86 RPM	86.33 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_325 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_325 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_384
Pan troglodytes	retro_ptro_298
Gorilla gorilla	retro_ggor_389
Macaca mulatta	retro_mmul_493

---

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,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000003895	5 retrocopies	retro_ptro_1764, retro_ptro_2146, retro_ptro_236, retro_ptro_298, retro_ptro_306,
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,