RetrogeneDB ID: retro_ecab_146

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:132598412..132598825(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBFA
• Ensembl ID: ENSECAG00000008292
• Aliases: None
• Description: ribosome binding factor A (putative) [Source:HGNC Symbol;Acc:26120]

Sequence

>retro_ecab_146
AGAAAAATGTTTTGGTATGAAAGTCTTTCCTTGGCATCTCACTTTTCCTCAAATCATGTGAGCTGGAATTCCTAATGAAG
AACACCTCAAAGGAAACCAAGAAAGAGGACCATGTGCACTTAAGGGGCCCGGATGGCCCTTCTCTATAAAACACTGACGG
ATTTGCTGGGCATTTCTGAAGTGAACCAAGAGATCTAAGACCCAAACATGGAGTTTTCCAAGGTGTCTCTTACTTGAGAC
CTCTCAGCTTGCTGTGTATATTGGAAGACAACTCTTTTTGCTAATAGAATGAGCACACTGAAGCCATCTCATAGAAAAGC
ACTGTACACATGAGGCATTATTTGATGTCTCAGCAGATCCTGAGGAATGAGCTGCCTATGGTTTTTGTCCTAGTCATACA
AAATGCAGCTCTG

Alignment

ORF - retro_ecab_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.12 %
• Parental protein coverage: 54.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKKFWYEGPSLSSH-LTYKPSQLEFLTKSTSKKTKKEDHVRLRALNG-LLYKALTDLLCTPEVSQEVYDL
          RK.FWYE..SL.SH.L..K...LEFL.K.TSK.TKKEDHV.LR...G.LLYK.LTDLL...EV.QE..D.
Retrocopy RKMFWYESLSLASH<LFLKSCELEFLMKNTSKETKKEDHVHLRGPDG>LLYKTLTDLLGISEVNQEI*DP

Parental  NLELSKVSLTSDFSACRVYWKTTLSAEQ-NSHTEATLRRSAAHVRHLLMSQQTLRNVPPIVFVQDKENAA
          N.E.SKVSLT.D.SAC.VYWKTTL.A...N.HTEA....S..H.RH.LMSQQ.LRN..P.VFV....NAA
Retrocopy NMEFSKVSLT*DLSACCVYWKTTLFANR<NEHTEAIS*KSTVHMRHYLMSQQILRNELPMVFVLVIQNAA

Parental  L
          L
Retrocopy L

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	8.80 RPM
SRP021940_cerebellum	0.00 RPM	14.23 RPM
SRP021940_embryo	0.00 RPM	25.42 RPM
SRP021940_placental_villous	0.00 RPM	7.12 RPM
SRP021940_synovial_membrane	0.00 RPM	13.67 RPM
SRP021940_testis	0.00 RPM	9.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_146 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_146 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1062

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036297	1 retrocopy	retro_btau_1031,
Cavia porcellus	ENSCPOG00000000170	1 retrocopy	retro_cpor_911,
Equus caballus	ENSECAG00000008292	1 retrocopy	retro_ecab_146 ,
Pan troglodytes	ENSPTRG00000010137	1 retrocopy	retro_ptro_1062,