RetrogeneDB ID: retro_ecab_688

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:29004011..29004308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTSF1
• Ensembl ID: ENSECAG00000013618
• Aliases: None
• Description: gametocyte specific factor 1 [Source:HGNC Symbol;Acc:26565]

Sequence

>retro_ecab_688
AATGTCACAAACAAATTGGCTACTTGTCCTTTCAATGCTCGCCACCAGGTTCCTTGACCGAAATCAGTCATCGTATCTCA
AGCTGTGATGACAAACTTGTATTGATCAGGATGTTGTCCACTAACCCAGGAAACCTGGATAAGGGCTCTGGCTGAGAGCA
CATGGCAGTGCCCTCCTTGGATGAAGTCTGGCATAAAGATTTGTGGAAACAGACCAGCACACCATGTCTAGGGCTCAGCC
AATTACTGTGGCAAGAACAGCCCTGCCAGCAACATACTTATGGAACATTAGAGTAAT

Alignment

ORF - retro_ecab_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.15 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DVANKLATCPFNARHQVP-RAEISHHISSCDDK-SCIEQDVVNQTRNLG-QETLAESTWQCPP-CDEDWD
          .V.NKLATCPFNARHQVP...EISH.ISSCDDK..CI.QDVV...R..G....LAESTWQCPP..DE.W.
Retrocopy NVTNKLATCPFNARHQVP<LTEISHRISSCDDK<TCIDQDVVH*PRKPG<IRALAESTWQCPP<LDEVWH

Parental  KDLWEQTSTPFVWGTTNYCGNNSP-ASNIVMEHKSN
          KDLW.QTSTP...G.........P.ASNI.MEH.SN
Retrocopy KDLWKQTSTPCL-GLSQLLWQEQP>ASNILMEH*SN

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
SRP021940_articular_cartilage	0.00 RPM	0.12 RPM
SRP021940_cerebellum	0.00 RPM	0.05 RPM
SRP021940_embryo	0.00 RPM	0.28 RPM
SRP021940_placental_villous	0.00 RPM	8.13 RPM
SRP021940_synovial_membrane	0.00 RPM	1.35 RPM
SRP021940_testis	0.06 RPM	170.22 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_688 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_688 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_377

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014260	3 retrocopies	retro_acar_135, retro_acar_143, retro_acar_92,
Ailuropoda melanoleuca	ENSAMEG00000000939	6 retrocopies	retro_amel_1420, retro_amel_324, retro_amel_338, retro_amel_639, retro_amel_724, retro_amel_796,
Bos taurus	ENSBTAG00000018085	1 retrocopy	retro_btau_1316,
Canis familiaris	ENSCAFG00000006465	2 retrocopies	retro_cfam_377, retro_cfam_592,
Choloepus hoffmanni	ENSCHOG00000001659	2 retrocopies	retro_chof_1261, retro_chof_950,
Callithrix jacchus	ENSCJAG00000018968	1 retrocopy	retro_cjac_904,
Dasypus novemcinctus	ENSDNOG00000001438	4 retrocopies	retro_dnov_2233, retro_dnov_2536, retro_dnov_256, retro_dnov_76,
Equus caballus	ENSECAG00000013618	2 retrocopies	retro_ecab_688 , retro_ecab_806,
Echinops telfairi	ENSETEG00000009310	1 retrocopy	retro_etel_1619,
Felis catus	ENSFCAG00000010156	5 retrocopies	retro_fcat_1252, retro_fcat_1302, retro_fcat_1543, retro_fcat_557, retro_fcat_940,
Loxodonta africana	ENSLAFG00000016318	1 retrocopy	retro_lafr_1185,
Macropus eugenii	ENSMEUG00000016206	1 retrocopy	retro_meug_942,
Microcebus murinus	ENSMICG00000008444	1 retrocopy	retro_mmur_842,
Myotis lucifugus	ENSMLUG00000012961	3 retrocopies	retro_mluc_1177, retro_mluc_1286, retro_mluc_56,
Mustela putorius furo	ENSMPUG00000005669	3 retrocopies	retro_mputfur_1249, retro_mputfur_155, retro_mputfur_62,
Otolemur garnettii	ENSOGAG00000017227	2 retrocopies	retro_ogar_2617, retro_ogar_3251,
Rattus norvegicus	ENSRNOG00000036831	1 retrocopy	retro_rnor_2525,
Tarsius syrichta	ENSTSYG00000004679	2 retrocopies	retro_tsyr_1437, retro_tsyr_1880,
Tursiops truncatus	ENSTTRG00000004470	1 retrocopy	retro_ttru_249,
Vicugna pacos	ENSVPAG00000007016	5 retrocopies	retro_vpac_103, retro_vpac_203, retro_vpac_223, retro_vpac_490, retro_vpac_95,