RetrogeneDB ID: retro_ecab_287

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 13:19396971..19397518(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM60A
• Ensembl ID: ENSECAG00000009655
• Aliases: None
• Description: family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]

Sequence

>retro_ecab_287
CAGAGTTGGTTTGGGTTGCATGAGACTCGTTCAGTAGACATCTGTAATGCCTGTGGCCTGCTTGTGAAAAGATGGAAGGA
ATTGCCAGAGGATCAAAAAAACCCTGGAATCAAGTGGTAGATACAAGAACAGGACCCAATCTAAAGATTACATTGAAACC
AAAGAAAGTGAACACTCTATCTGGAAACAGGATAAAAAGCAACCATGTCAGTAAACTGCAGAAGGAATTCAAACGTCACA
ATTCTCATGCTCATGGTAACACCTCAAGTTCCTCCCCAGCTCACTCTCCTTGTTATAGTAACCAATTGGATGATGGCTCG
GATACAGCGATGGCTTCTGGCTTTAGCAGAACACCAGTTTTTCCTTTTTAGATCTCACATACTGGAAAAGACAGAAAATA
TGTTGTGGGATTATCTATAAAGGCCGTTTTGGGGAAGTCCTCATCAACACACATCTATTCAAGCCTTGCTGCAGCAATAA
GGAAGCAGCTGCTGAGAAGCAGGAGGAGCAGGGGCCCGAGCCTCTGAACATCTCCACTCAGGAGTGG

Alignment

ORF - retro_ecab_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 82.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QSCFGLHETRSGDICNACVLLVKRWKKLPA-GSKKNWNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQ
          QS.FGLHETRS.DICNAC.LLVKRWK.LP..GSKK.WN.VVD.R.GP.LK.TLKPKKV.TLSGNRIKSN.
Retrocopy QSWFGLHETRSVDICNACGLLVKRWKELPE<GSKKPWNQVVDTRTGPNLKITLKPKKVNTLSGNRIKSNH

Parental  ISKLQKEFKRHNSDAHSTTSSASPAQSPCYSNQSDDGSDTEMASGSNRTPV-FSFLDLTYWKRQKICCGI
          .SKLQKEFKRHNS.AH..TSS.SPA.SPCYSNQ.DDGSDT.MASG..RTPV.FSFLDLTYWKRQKICCGI
Retrocopy VSKLQKEFKRHNSHAHGNTSSSSPAHSPCYSNQLDDGSDTAMASGFSRTPV<FSFLDLTYWKRQKICCGI

Parental  IYKGRFGEVLIDTHLFKPCCSNKKAAAEKPEEQRPEPLPLPPQEW
          IYKGRFGEVLI.THLFKPCCSNK.AAAEK.EEQ.PEPL....QEW
Retrocopy IYKGRFGEVLINTHLFKPCCSNKEAAAEKQEEQGPEPLNISTQEW

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	0.47 RPM
SRP021940_cerebellum	0.10 RPM	0.42 RPM
SRP021940_embryo	0.10 RPM	15.16 RPM
SRP021940_placental_villous	0.00 RPM	7.60 RPM
SRP021940_synovial_membrane	0.05 RPM	1.95 RPM
SRP021940_testis	0.13 RPM	1.47 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_287 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_287 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Dasypus novemcinctus	ENSDNOG00000016873	2 retrocopies	retro_dnov_1674, retro_dnov_2668,
Equus caballus	ENSECAG00000009655	2 retrocopies	retro_ecab_287 , retro_ecab_385,
Erinaceus europaeus	ENSEEUG00000012617	2 retrocopies	retro_eeur_350, retro_eeur_372,
Echinops telfairi	ENSETEG00000002888	2 retrocopies	retro_etel_1087, retro_etel_427,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Microcebus murinus	ENSMICG00000003460	2 retrocopies	retro_mmur_1176, retro_mmur_409,
Otolemur garnettii	ENSOGAG00000008927	4 retrocopies	retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,