RetrogeneDB ID: retro_ecab_532

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 20:1258425..1258819(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSECAG00000009882
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_ecab_532
CTGATTTCATCAGTTGACCCACAGTTCTGAAACTCACCAAAGTGGATGAACAAGTCTATTCCGACTTCTGGGAAAATTCT
GAGAAACTCAGGATAGATGTTTTTGACTTAGAAGAGCTCAACTCAGAATTGGCAAAAGAGAAGTGGAGGCCATTCCCCCA
GCAGTTTGATGGGATTGCAGAAGACTTCGACTATAGTATTTTGCTGCAACTGTACTGTTTTCAGGCCTACATTGGAGGAA
AACACCATTTTGCCTGCAGGATACAATTTTTTGCCATTGAAATTGCTCAAAATTGAGAAGGCTATAGCAAAGCAGTTTAC
ACTAGTGTTCAGGACAGAGAAGGAGAGAAAGGAGCCAAAACAGAAGAAAGAATGGAGCTGACTGTGGAGGAGAA

Alignment

ORF - retro_ecab_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.32 %
• Parental protein coverage: 67.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LISSVDPQF-LKLTKVDDQIYSEFRENFEKLRIDVLDPEELKSESAKEKWRPFCLKFDGIVEDFNYGTLL
          LISSVDPQF.LKLTKVD.Q.YS.F.EN.EKLRIDV.D.EEL.SE.AKEKWRPF...FDGI.EDF.Y..LL
Retrocopy LISSVDPQF<LKLTKVDEQVYSDFWENSEKLRIDVFDLEELNSELAKEKWRPFPQQFDGIAEDFDYSILL

Parental  RLDCSQGYT-EENTI-FAPRIQFFAIEIARNREGCNKAVYTSVKDKE-EKGA-NNGGEKGADSGGE
          .L.C.Q.Y..EENTI.FA.RIQFFAIEIA.N.EG..KAVYTSV.D.E.EKGA..N....GAD.GGE
Retrocopy QLYCFQAYI>EENTI<FACRIQFFAIEIAQN*EGYSKAVYTSVQDREGEKGA<QNRRKNGADCGGE

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	2.36 RPM
SRP021940_cerebellum	0.00 RPM	2.65 RPM
SRP021940_embryo	0.00 RPM	10.64 RPM
SRP021940_placental_villous	0.00 RPM	3.61 RPM
SRP021940_synovial_membrane	0.00 RPM	3.95 RPM
SRP021940_testis	0.00 RPM	1.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_532 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_532 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532 ,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,