RetrogeneDB ID: retro_ecab_1095

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:124060324..124060561(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPH3
• Ensembl ID: ENSECAG00000016591
• Aliases: None
• Description: diphthamide biosynthesis 3 [Source:HGNC Symbol;Acc:27717]

Sequence

>retro_ecab_1095
AAGGTGGGAATCATGGACTTGCAATATAATCATTCCTTGGAGATGTATTTCTACCCCTGCACATGTAGGGATAACTTCTT
TGGGCATCTCATCCTCACCAAGGAAGAGTTGGAGAATGGGGAAAATGTGGCTACGTGTCCTGGATGTTCTCTCATTATAA
AAGTGATTGATGACAAAGGTCAGTTTATGTGCAGAGAAACTATCCCAGCTCCTTCCACCAGCAAATAATTGGTTGAA

Alignment

ORF - retro_ecab_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.82 %
• Parental protein coverage: 91.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVEIEDFQYDEDSETYFYPCPCGDNF----CITKEDLENGEDVATCPSCSLIIKVIYDKDQFMCGETVPA
          .V.I.D.QY....E.YFYPC.C.DNF......TKE.LENGE.VATCP.CSLIIKVI.DK.QFMC.ET.PA
Retrocopy KVGIMDLQYNHSLEMYFYPCTCRDNFFGHLILTKEELENGENVATCPGCSLIIKVIDDKGQFMCRETIPA

Parental  PSTNKELVK
          PST.K.LV.
Retrocopy PSTSK*LVE

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	2.30 RPM
SRP021940_cerebellum	0.00 RPM	2.08 RPM
SRP021940_embryo	0.00 RPM	6.83 RPM
SRP021940_placental_villous	0.00 RPM	3.37 RPM
SRP021940_synovial_membrane	0.00 RPM	2.17 RPM
SRP021940_testis	0.00 RPM	9.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1095 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1095 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003916	2 retrocopies	retro_btau_797, retro_btau_967,
Canis familiaris	ENSCAFG00000005881	1 retrocopy	retro_cfam_273,
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Equus caballus	ENSECAG00000016591	1 retrocopy	retro_ecab_1095 ,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Felis catus	ENSFCAG00000006355	1 retrocopy	retro_fcat_656,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,