RetrogeneDB ID: retro_ecab_948

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:12279397..12279784(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSECAG00000012409
• Aliases: None
• Description: SAR1 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:10535]

Sequence

>retro_ecab_948
ATGTCCTTCATGTAACGTTGGATTTACAGTGGTTTCAGCAGTTTGCAACAGTTTTTAGGATTACATAACAAGATTGGTAA
ATTGGTATTTCGTGGATTGAATAATGTGGGGAAAACAACATTGCCACACATGCTAAAAGATGACAGACTTGGACAACATG
TCCCGACGTCACACATCCCACTTCACGAGAACTAACCATTTCTGGCATGACCTTTACAATTTTTGATTTGGGTGCACATG
TTCAAGCTCAAAGAGTATGGAAAAACTACCTTTCTGCTATCAATGGCATCGTATTTCTCGTGGATTGTGCAAACCGTGAA
AGGCTGTTAGAATCAAAACAAGAAGTTGATTCACTAGTTGATAAGTGATACCATTGCTAACATGCCT

Alignment

ORF - retro_ecab_948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.57 %
• Parental protein coverage: 64.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFIFDWIYSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLH-PTSE-ELTIAG
          MSF...WIYSGFSS..QFLGL..K.GKLVF.GL.N.GKTTL.HMLKDDRLGQHVPT.H.P..E.ELTI.G
Retrocopy MSFM*RWIYSGFSSLQQFLGLHNKIGKLVFRGLNNVGKTTLPHMLKDDRLGQHVPTSHIPLHE<ELTISG

Parental  MTFTTFDLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSL-MTDETIANVP
          MTFT.FDLG.HVQA.RVWKNYL.AINGIVFLVDCA..ERLLESK.E.DSL.....TIAN.P
Retrocopy MTFTIFDLGAHVQAQRVWKNYLSAINGIVFLVDCANRERLLESKQEVDSL>LISDTIANMP

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	16.82 RPM
SRP021940_cerebellum	0.00 RPM	16.31 RPM
SRP021940_embryo	0.00 RPM	11.64 RPM
SRP021940_placental_villous	0.00 RPM	30.45 RPM
SRP021940_synovial_membrane	0.00 RPM	9.36 RPM
SRP021940_testis	0.00 RPM	15.28 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_948 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_948 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_948 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Equus caballus	ENSECAG00000012409	1 retrocopy	retro_ecab_948 ,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Macaca mulatta	ENSMMUG00000004417	3 retrocopies	retro_mmul_1825, retro_mmul_2507, retro_mmul_304,