RetrogeneDB ID: retro_ecab_612

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:7444249..7444893(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP5
• Ensembl ID: ENSECAG00000013514
• Aliases: None
• Description: dual specificity phosphatase 5 [Source:HGNC Symbol;Acc:3071]

Sequence

>retro_ecab_612
CTGTGTCAGCCAGCAGCAGCCCTGTGGGTCTACTTGCTCCAAGGGGGGTATGAGACCTTTTACTCAGAAGCTCCTGAGTG
TTGTGTGAATTTAAAACCCATTTCACAAGAGGAGGTTGAAATGAAAAAGCCCTCATTAACCAGTGTGGGAAACCAGCACT
TGACACCAGCTACAAGCTGACTTCTGAGCAGGGTGGCCCAGTTGCAATCCTTCTATGCCTCAACTTTGGAAGTGCCCACT
GTGCATCCAAGTGCAAAATCCACACCAGCCTGAACATCATGGTCCTGCTGAATGTCTCTCAGCAGCCCTCCAAGGTCTGT
GTGGCCCACCTGCAATACTAATGGACCCCTGTGGAAGACAGCCACGTGATTGACGTTAACTCCCACTTTCGAGAAGCAAT
AGACTTCATTGACTGTTTAGGGGGAAGGGAGCAAAATCCTGGTCCTCTGTGAGACTTGGATCTCCTGTTTACACTCCATC
TGCAAGGATTATCTCATGAAGACCAAGCAGGTGGCCTGAAGGACGCCTTGGACTGCATCGAGCAGAAGAATATGATCTCA
CCCAACTTTGGCTTCATGGACCAACTTCTGCAGTATGAATCTGACATGTTCCACATCCACCCCAAGGCTCCCTTCTGCCA
AGGG

Alignment

ORF - retro_ecab_612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.74 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LCLPARRPAVYFLKGGYETFYSEYPECCVDVKPISQEKIE-TERALISQCGKPVLNISYRPVYDQGGPVE
          LC.PA....VY.L.GGYETFYSE.PECCV..KPISQE..E..E.ALI.QCGKP.L..SY.....QGGPV.
Retrocopy LCQPAAALWVYLLQGGYETFYSEAPECCVNLKPISQEEVE<NEKALINQCGKPALDTSYKLTSEQGGPVA

Parental  ILPFLYLGSAYHASECEFLANLHITALLNVSRRASEACTTRLHYKWIPVEDSHTADISSHFQEAIDFIDC
          IL..L..GSA..AS.C.....L.I..LLNVS...S..C...L.Y.W.PVEDSH..D..SHF.EAIDFIDC
Retrocopy ILLCLNFGSAHCASKCKIHTSLNIMVLLNVSQQPSKVCVAHLQY*WTPVEDSHVIDVNSHFREAIDFIDC

Parental  V-REKG-GKVLVHCEAGISRSPTICMAYLMKTKQFR-LKDAFDYIKQRRSVISPNFGFMGQLLQYESEIL
          ..R.KG..K.LV.CE..IS....IC..YLMKTKQ...LKDA.D.I.Q....ISPNFGFM.QLLQYES...
Retrocopy L<RGKG<SKILVLCETWISCLHSICKDYLMKTKQVA<LKDALDCIEQ-KNMISPNFGFMDQLLQYESDMF

Parental  PSTPTPQAPSCQG
          ...P...AP.CQG
Retrocopy HIHP--KAPFCQG

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	0.59 RPM
SRP021940_cerebellum	0.00 RPM	27.37 RPM
SRP021940_embryo	0.00 RPM	2.40 RPM
SRP021940_placental_villous	0.00 RPM	11.21 RPM
SRP021940_synovial_membrane	0.00 RPM	1.78 RPM
SRP021940_testis	0.00 RPM	22.32 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_612 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_612 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_612 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015745	1 retrocopy	retro_amel_1630,
Dasypus novemcinctus	ENSDNOG00000001858	1 retrocopy	retro_dnov_1665,
Equus caballus	ENSECAG00000013514	2 retrocopies	retro_ecab_188, retro_ecab_612 ,