RetrogeneDB ID: retro_ecab_1059

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:39057709..39058487(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSECAG00000015001
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_ecab_1059
ACAAGGAGACAGCCAGGGTGCAGAGGAGTATGCATTGCCTGCTGAGATGTACTGAAGTGGGAGTCTGCTGCCAGTGAAAT
CCAAGCTGATACAAAGAACTCTCAGGTGATGGTGCTGAAACTGGACCTGTCCGATACCAAATCCATCCAAGTCTTTGCTG
AAGGCTTTGTGGCAGAGGAAAAGCAGCTCCGTATTCTGATCAACAATGCAAGAGTGATGATGTGTCCATATTCCAAGACA
ACCAATGGCTTTGAAACCCACCTGGAAGTCAACCACCTGGGCCACTTCCTTCTCACCCACTTGCTCCTGGAGTGGCTGAA
GGAGTCTGCTCCTGCCGGGTGGTGGACCTGTCATCGGTGGCCCACCATGCTGGCAAGATTCGTTTCTACAACCTCTAGAG
TGAGAACTGCTACAGCTGGAGTTTTGCTTACTTCCACAGCAAGCTGGCCAATGCGCTTTTTACTCAGGAGCTGGCCAAGA
AGCTCCAAGGCACAGGGGTCACCACCTACGCAGTGCACCCAGGCATCATCCACTCTGAGCTGGTCTGACACTTCTTCCTG
CGTGCCTGCTATGGTGGCTCTTCTTCCCCTTCGTCAAGTCGGCCTAGGAGGGGGCACAGACCAGCTTGCACTGCACCCTG
GCTGAGGGCCTGGAGTCCCTGAGTGGCGAGCACTTCAGTGACTGCGAGAGGACCTGAGTGTCTCCAAAGGCCTGAAATAA
CAAAATAGCTGAGTGCCTGCAGATCGCCAGCTGTGAGCTTCTAGGAATCCAGGGAGAG

Alignment

ORF - retro_ecab_1059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.21 %
• Parental protein coverage: 82.91 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TARELARRGARVYIACRDVLKGESAASEIRADTKNSQVLVRKLDLSDTRSIRAFAEGFLAEEKQLHILIN
          T.R....RG..V.IAC.DVLK.ESAASEI.ADTKNSQV.V.KLDLSDT.SI..FAEGF.AEEKQL.ILIN
Retrocopy TRRQPGCRG--VCIAC*DVLKWESAASEIQADTKNSQVMVLKLDLSDTKSIQVFAEGFVAEEKQLRILIN

Parental  NAGVMMFSHSKTTDGFEINLGVNHLGHFLLTYLLLERLKESAPA-RVVNLSSVIHHLGKIHFHNFRGEEP
          NA.VMM...SKTT.GFE..L.VNHLGHFLLT.LLLE.LKESAPA.RVV.LSSV.HH.GKI.F.N...E..
Retrocopy NARVMMCPYSKTTNGFETHLEVNHLGHFLLTHLLLEWLKESAPA<RVVDLSSVAHHAGKIRFYNL*SENC

Parental  YRWGFAYCHSKLANLLFTRELAKRIQGTGVTTYAVHPGIVRSELARHSFL-CCLFWRLFSYFLKSVQEGA
          Y.W.FAY.HSKLAN.LFT.ELAK..QGTGVTTYAVHPGI..SEL..H.FL..CL.W.LF..F.KS..EGA
Retrocopy YSWSFAYFHSKLANALFTQELAKKLQGTGVTTYAVHPGIIHSELV*HFFL<ACLLWWLFFPFVKSA*EGA

Parental  QTSLHCALAEGLEPLSGKYFSDCKRTWVSPRARDNKTAQRLWNVSCELLGIQWE
          QTSLHC.LAEGLE.LSG..FSDC.RT.VSP.A..NK.A..L...SCELLGIQ.E
Retrocopy QTSLHCTLAEGLESLSGEHFSDCERT*VSPKA*NNKIAECLQIASCELLGIQGE

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	5.37 RPM
SRP021940_cerebellum	0.00 RPM	0.62 RPM
SRP021940_embryo	0.00 RPM	0.97 RPM
SRP021940_placental_villous	0.00 RPM	1.11 RPM
SRP021940_synovial_membrane	0.00 RPM	1.07 RPM
SRP021940_testis	0.00 RPM	0.90 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1059 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1059 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_2068

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015001	1 retrocopy	retro_ecab_1059 ,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,