RetrogeneDB ID: retro_ecab_459

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 19:21723649..21724128(+)
• Located in intron of: ENSECAG00000008905

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF115
• Ensembl ID: ENSECAG00000009030
• Aliases: None
• Description: ring finger protein 115 [Source:HGNC Symbol;Acc:18154]

Sequence

>retro_ecab_459
ATAATACAACGGATCTTTGAAGGATTCTTTGCAAATTCTGCAATTCCTGGATCCCTACACCCTTTCACCTGGAGCGGGAT
GCTGCACTCCAACCCTGGGGACTATGCCTGGGGTCAGACAGGGCTCGATGCCATTGTAACCCAGCTTTTAGGACAAGTGG
AAAATACAGGGCCTCCCCCAGCTGACAAGGAAAAGATCACATCTCTTCCAACAGTGACAGTAACTCAGGAACAAGTTGAC
ATGGGTTTAGAGTGTCCAGTATATAAAGAAGATTACACAGGTGAAGAGGAAGTCTGGCAGTTACCCTGCAAACACTTCTT
CCACAGCAGTTGTATTGTGCCGTGGTTAGAATTGCATGACGCATGTGCTGTATGTAGGAAGAGCTTAAATGGTGAGGACT
CTGCTCGGCAAACCCAGAGCTCTGAGGCCTCTGCAAGCAACAGATTTAGCGACAGCCAGCACATGACTGATGGACTTTC

Alignment

ORF - retro_ecab_459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.12 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIQQIFAGFFANSAIPGP-HPFTWSGMLHSNPGDYAWGQTGLDAIVTQLLGQLENTGPPPADKEKITSLP
          IIQ.IF.GFFANSAIPG..HPFTWSGMLHSNPGDYAWGQTGLDAIVTQLLGQ.ENTGPPPADKEKITSLP
Retrocopy IIQRIFEGFFANSAIPGSLHPFTWSGMLHSNPGDYAWGQTGLDAIVTQLLGQVENTGPPPADKEKITSLP

Parental  TVTVTQEQVDMGLECPVCKEDYTVEEEVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSLNGEDSTRQTQS
          TVTVTQEQVDMGLECPV.KEDYT.EEEV.QLPC.HFFHSSCIVPWLELHD.C.VCRKSLNGEDS.RQTQS
Retrocopy TVTVTQEQVDMGLECPVYKEDYTGEEEVWQLPCKHFFHSSCIVPWLELHDACAVCRKSLNGEDSARQTQS

Parental  SEASASNRFSSDSQ-LHDRWTF
          SEASASNRF.SDSQ..HD.WTF
Retrocopy SEASASNRF-SDSQ<AHD*WTF

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	0.47 RPM	6.79 RPM
SRP021940_cerebellum	0.52 RPM	20.41 RPM
SRP021940_embryo	0.54 RPM	14.45 RPM
SRP021940_placental_villous	0.34 RPM	14.10 RPM
SRP021940_synovial_membrane	0.47 RPM	16.69 RPM
SRP021940_testis	0.26 RPM	10.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_459 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009030	1 retrocopy	retro_ecab_459 ,
Macropus eugenii	ENSMEUG00000002500	1 retrocopy	retro_meug_1546,
Oryctolagus cuniculus	ENSOCUG00000003055	1 retrocopy	retro_ocun_1138,
Pteropus vampyrus	ENSPVAG00000014487	13 retrocopies	retro_pvam_1039, retro_pvam_1096, retro_pvam_1111, retro_pvam_1293, retro_pvam_1295, retro_pvam_1442, retro_pvam_730, retro_pvam_733, retro_pvam_759, retro_pvam_796, retro_pvam_806, retro_pvam_849, retro_pvam_964,
Tarsius syrichta	ENSTSYG00000004867	2 retrocopies	retro_tsyr_1734, retro_tsyr_1870,