RetrogeneDB ID: retro_ecab_683

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 28:357121..358089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC20
• Ensembl ID: ENSECAG00000016465
• Aliases: None
• Description: zinc finger, DHHC-type containing 20 [Source:HGNC Symbol;Acc:20749]

Sequence

>retro_ecab_683
TGCGTGGTTATGCTTTCTTGAAATGGAGAAAACGGAAAGGTCGTTGTTTACCTTGTGGGTTTCCATCTGTTCTTGTATGT
TTGTATAGTCCTATTGGATGACAATTTTTCACATCTCCCGCTTCCCCCTCCAAAGACTTCTACTTGTCCAGTTCTGAAAA
GGAACGTTATGAAAAGGAATTCAACCAAGAAAGACAACAAGAAATTTTGAGAAGAGCAGCAAGTGACTTACCCATCTACA
CCCTGTCAGCTGCAAGGACCGTCAGATATTGTGAAAGATGTCAGTTGATTAACATCTGACGTGTGCATCACTGCTCAGCA
TGTGATATATGTGTTCTTAAGATGGATCATCACTGTCCTTGGGTGAATAACTGTGTGGGATTTTCTAATTATAAATTATT
CCTGCTGTTTTTATTATATTGCCTTTTCATAGCTACAACAGTTTTACAGTGCTTTATAAAATTTTGGACGAATGAACTCT
CAGCTACACGTGCAAAATTCCACGTACTTTTTCTTTTCTTTGTGTTTACAATGTTCTTCATCAGCGTCCTGTCGCTGTTC
AGCCACCACTGCTGGCTAGTTGGGAAAAATAGAACAATAGAATCATTCCGTGCACCCACATTTTCCTATGGACCTGATGG
AAATGGTTTCTCTCTTGGATGCAGTAAAAATTGGAGACAAGTCTTTGGTGATGAAAAGAAATATTGGCTACTTCCAATAT
TTTCAAGTTTGGGTGATGGTTGCAGTTTCCCAACTCTCCTGGTGGGGATGGATCCAGAACAAGCTTCTGTTTCAAACCAA
AACAAATATGCCAGAAGTATTGGCTCAAATCAACCCTTTCCTGTCAAACCACTTAGTGAATCGAAAAACCGGTTATTGGA
CAGTGAGTCTCAGTGGCTAGAGAACGGATCTGAAAAAAGCACCGTCAGATCAGGGACAAATAACCATGTTACAGTGGCAA
TAGAAAAT

Alignment

ORF - retro_ecab_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.61 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CIFTVLFNRCSGKAVVYLV-GFHLFFV-MFVWSYWMTVF-TSPASPSKEFYLSSSDKERYEKEFNQERQQ
          C......N...GK.VVYLV.GF....V.MFV.SYWMT.F.TSPASPSK.FYLSSS.KERYEKEFNQERQQ
Retrocopy CVVMLS*NGENGKVVVYLV<GFPSVLV<MFV*SYWMTIF>TSPASPSKDFYLSSSEKERYEKEFNQERQQ

Parental  EILRRTARDLPISTLSAARTIRYCERCQLIKPDRAHHCSACDICVLKMDHHCPWVNNCVGFSNYKFFLLF
          EILRR.A.DLPI.TLSAART.RYCERCQLI...R.HHCSACDICVLKMDHHCPWVNNCVGFSNYK.FLLF
Retrocopy EILRRAASDLPIYTLSAARTVRYCERCQLINI*RVHHCSACDICVLKMDHHCPWVNNCVGFSNYKLFLLF

Parental  LLYSLLYCLFVATTVLQCFIKFWTNELSATRAKFHVLFLFFVSTMFFISVLSLFSYHCWLVGKNRTTIES
          ....LLYCLF.ATTVLQCFIKFWTNELSATRAKFHVLFLFFV.TMFFISVLSLFS.HCWLVGKNR.TIES
Retrocopy ----LLYCLFIATTVLQCFIKFWTNELSATRAKFHVLFLFFVFTMFFISVLSLFSHHCWLVGKNR-TIES

Parental  FRAPTFSYGPDGNGFSLGCSKNWRQVFGDEKKYWLLPIFSSLGDGCSFPTRLVGMDPEQASVSNQNEYAR
          FRAPTFSYGPDGNGFSLGCSKNWRQVFGDEKKYWLLPIFSSLGDGCSFPT.LVGMDPEQASVSNQN.YAR
Retrocopy FRAPTFSYGPDGNGFSLGCSKNWRQVFGDEKKYWLLPIFSSLGDGCSFPTLLVGMDPEQASVSNQNKYAR

Parental  SIGSNQPFPVKPLSESKNRLLDSESQWLENGSEESTVRSGTNNHVTVAIEN
          SIGSNQPFPVKPLSESKNRLLDSESQWLENGSE.STVRSGTNNHVTVAIEN
Retrocopy SIGSNQPFPVKPLSESKNRLLDSESQWLENGSEKSTVRSGTNNHVTVAIEN

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	0.12 RPM	8.50 RPM
SRP021940_cerebellum	0.10 RPM	5.76 RPM
SRP021940_embryo	0.08 RPM	10.31 RPM
SRP021940_placental_villous	0.19 RPM	10.15 RPM
SRP021940_synovial_membrane	0.19 RPM	10.82 RPM
SRP021940_testis	0.32 RPM	22.38 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_683 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012155	2 retrocopies	retro_chof_1627, retro_chof_2008,
Cavia porcellus	ENSCPOG00000011489	1 retrocopy	retro_cpor_303,
Equus caballus	ENSECAG00000016465	1 retrocopy	retro_ecab_683 ,
Homo sapiens	ENSG00000180776	1 retrocopy	retro_hsap_1211,
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829,
Tarsius syrichta	ENSTSYG00000003013	1 retrocopy	retro_tsyr_998,