RetrogeneDB ID: retro_ecab_709

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 3:12436917..12437397(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSECAG00000005250
• Aliases: None
• Description: STARD3 N-terminal like [Source:HGNC Symbol;Acc:19169]

Sequence

>retro_ecab_709
AAGGAAACGAGTGGCATATCCAGTGTCTGAAGGACTTTCTATTTGTTTATCACCTTTGATTTCTTAACTGTAAACTTAAC
AGGAAAAACATAGTTGAATACAAATAGAAAAATAGAAAAAGTTTTAGTGAAGGAGAGAGGGCAGTATGTTTAGTATTTCC
TTTATTCCAGTGGATTTCTTTCGAAAATATTTAATTGGAAGCATTAATGCTTGCATATGCAGTATGTAACTACCACAAGC
AGGCTGTGGCATTGGCGATGGCAGTGACCATGGTCTTTTTTATTAGCACAGGTGTTCCTCTCCTAGCTTTTCTCTCAGGG
TGCTTTCGGATCTGTGCTGCCTATTTCATTGATACTTTCCTGGACTGAGATCTGGTGCATGGATTTCAAAGTCTTGACAC
AAGGAACAGAAGTGGAAATCAGATCCCTCTTAGTTCAGGATGCCTCAGAGAAAGCAAGCTTTATACAACCTTGTGGTCTT

Alignment

ORF - retro_ecab_709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.1 %
• Parental protein coverage: 68.8 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  REKKGISDVRRTFCLFVTFDLLFVTLLWIIELNVNGGIENTLEKEVVQYDYYSSYFDIFLLAVFRFK-VL
          .E..GIS.V.RTF.LF.TFD.L.V.L.....LN.N..IE..L.KE..QY..Y..Y...FL...F..K..L
Retrocopy KETSGISSV*RTFYLFITFDFLTVNLTGKT*LNTNRKIEKVLVKERGQYV*YFLYSSGFLSKIFNWK<AL

Parental  ILAYAVCRLRHWWAIALTTAVTS-AFLLAKVILSKLFSQGAFGYVLPIISFILAWIETWFLDFKVLPQEA
          .LAYAVC...H..A.AL..AVT...FLLA.V.LS.LFSQGAFG.VLPI.S.IL.W.E.W..DFKVL.Q..
Retrocopy MLAYAVCNY-HKQAVALAMAVTM>SFLLAQVFLS*LFSQGAFGSVLPI-SLILSWTEIWCMDFKVLTQGT

Parental  EEENRLLIVQDASERAALI-PGGL
          E.E.R.L.VQDASE.A..I.P.GL
Retrocopy EVEIRSLLVQDASEKASFIQPCGL

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	6.91 RPM
SRP021940_cerebellum	0.00 RPM	28.67 RPM
SRP021940_embryo	0.00 RPM	13.94 RPM
SRP021940_placental_villous	0.00 RPM	15.92 RPM
SRP021940_synovial_membrane	0.00 RPM	12.33 RPM
SRP021940_testis	0.00 RPM	13.24 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_709 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709 ,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,