RetrogeneDB ID: retro_ecab_386

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:55884774..55885374(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BABAM1
• Ensembl ID: ENSECAG00000017099
• Aliases: None
• Description: BRISC and BRCA1 A complex member 1 [Source:HGNC Symbol;Acc:25008]

Sequence

>retro_ecab_386
TCCAACACTGAGGGGGCTGAGGACCAGGCACTGGAGGCCCAGGCCAGGCTGGGCAGCCACAGTAAGGCAGAGGATGAGGC
AGCCAGTGCTGATGAGGACTCCGAGCCCTCCAGGAGCTGGCTCCAATCCCTGGCAGGAGTCCCTGCTTGTCCCTGAGGTC
CAGGTGCAGATGCCAACGGCCAACTGTCCAGAAGGTGATCATCTGCCTGGACCTGTTGAAGGAAATGTTGCTGCTAAAGC
TGGAGTCGTTCAACAGCACCAAGATCAACGTGCTCAACGTCTCCCAGGAGATGAGGATAAAATACAAGAACAAAAGCCAC
GAATTCAGGCTGGTGGTGCTGAACGAGGACACAGCCTGGCTGTCTGGCCTGACCTCCAGCCCCCACAAGCACGGCAGCTG
CCTCTAGACCTGGAGATAGCCTTTTGTTCCATCTTCAATCTAGAAGGTCTCTTCAGCCTCATCCAGAAGAAGACTGAGCT
GCCAGTCACTAAGCACTTGTAGACGATCCCCTGCCAAGTGTGGTCCACACCATCCTTGTCTACAGCTGTTTGCTGTGCCA
GCCCCAGGTCTCCCTGCAGCGAGTGAAGAAATGTTCCAGG

Alignment

ORF - retro_ecab_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.25 %
• Parental protein coverage: 66.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SNPEGAEDRALGAQASVGSRSEGEGEAASADDG-TPNPPGAG-PKPWQVPPPAPEIQVRTPRVNCPEKVI
          SN.EGAED.AL.AQA..GS.S..E.E.A...D..TP.PPGAG.P.P...P........R..R.....KVI
Retrocopy SNTEGAEDQALEAQARLGSHSKAEDE-AASADE>TPSPPGAG>PIPGRSPCLSLRSRCRCQRPTV-QKVI

Parental  LCLDLSEEMALPKLESFNGSKTNALNVSQKMIEMFVRTKHKIDKSHEFALVVVNDDIAWLSGLTSDPREL
          .CLDL..EM.L.KLESFN..K....NV.....EM....K....KSHEF.LVV.N.D.AWLSGLTS.P...
Retrocopy ICLDLLKEMLLLKLESFNSTK---INVLNVSQEMRIKYKN---KSHEFRLVVLNEDTAWLSGLTSSPHKH

Parental  CSCL-YDLETASCSAFNLEGLVSLIQQKTELPVTENVQTI-PPPYVIRTILVYSRPPCQPQHGVTRVPNA
          .SCL..DLE.A.CS.FNLEGL.SLIQ.KTELPVT....TI.P.P.V..TILVYS...CQPQ....RV...
Retrocopy GSCL<LDLEIAFCSIFNLEGLFSLIQKKTELPVTKHL*TI<PLPSVVHTILVYSCLLCQPQVSLQRVKKC

Parental  GK
          ..
Retrocopy SR

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	46.57 RPM
SRP021940_cerebellum	0.00 RPM	89.53 RPM
SRP021940_embryo	0.05 RPM	103.70 RPM
SRP021940_placental_villous	0.00 RPM	54.08 RPM
SRP021940_synovial_membrane	0.00 RPM	69.51 RPM
SRP021940_testis	0.00 RPM	100.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_386 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_386 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017099	1 retrocopy	retro_ecab_386 ,